Expanded pore particles and delivery methods thereof

ABSTRACT

The present invention relates to a construct including a porous core, a cargo, and a spacer disposed between the core and the cargo. In some examples, the construct further includes an outer layer composed of a lipid, a polymer, or a combination thereof. Methods of making and employing such constructs are also described herein.

CROSS-REFERENCE TO RELATED APPLICATION

This application claims the benefit of U.S. Provisional Application No. 62/562,931, filed Sep. 25, 2017, which is hereby incorporated by reference in its entirety.

STATEMENT OF GOVERNMENT INTEREST

This invention was made with Government support under Contract No. DE-NA0003525 awarded by the United States Department of Energy/National Nuclear Security Administration. The Government has certain rights in the invention.

REFERENCE TO A SEQUENCE LISTING APPENDIX

A sequence listing appendix including an ASCII formatted file accompanies this application. The appendix includes a file named “SD14205_ST25.txt,” created on Sep. 25, 2018 (size of 164 kilobytes), which is hereby incorporated by reference in its entirety.

FIELD OF THE INVENTION

The present invention relates to a construct including a porous core, a cargo, and a spacer disposed between the core and the cargo. In some examples, the construct further includes an outer layer composed of a lipid, a polymer, or a combination thereof. Methods of making and employing such constructs are also described herein.

BACKGROUND OF THE INVENTION

Efficacious delivery of therapeutic agents still remains a challenge for certain classes of agents. For instance, due to delivery efficiency, certain gene-editing agents display effectiveness in cellular assays but show reduced efficacy in vivo. Thus, there is a need for additional delivery constructs that can be configured to accommodate such agents.

SUMMARY OF THE INVENTION

The present invention relates, in part, to a construct including a core, a cargo, and a spacer disposed between the core and the cargo. In particular embodiments, the core includes a plurality of pores, in which an average dimension of the pores is sufficient large enough to accommodate a large cargo. In some embodiments, the average dimension is greater than about 5 nm (e.g., of from about 5 nm to 35 nm, including from 5 nm to 10 nm, 5 nm to 15 nm, 5 nm to 20 nm, 5 nm to 25 nm, 5 nm to 30 nm, 8 nm to 10 nm, 8 nm to 15 nm, 8 nm to 20 nm, 8 nm to 25 nm, 8 nm to 30 nm, 8 nm to 35 nm, 10 nm to 15 nm, 10 nm to 20 nm, 10 nm to 25 nm, 10 nm to 30 nm, 10 nm to 35 nm, 12 nm to 15 nm, 12 nm to 20 nm, 12 nm to 25 nm, 12 nm to 30 nm, 12 nm to 35 nm, 15 nm to 20 nm, 15 nm to 25 nm, 15 nm to 30 nm, 15 nm to 35 nm, 18 nm to 20 nm, 18 nm to 25 nm, 18 nm to 30 nm, 18 nm to 35 nm, 20 nm to 25 nm, 20 nm to 30 nm, 20 nm to 35 nm, 25 nm to 30 nm, 25 nm to 35 nm, or 30 nm to 35 nm).

In some embodiments, the core is a mesoporous nanoparticle (e.g., a mesoporous silica nanoparticle). In particular embodiments, the core has a dimension (e.g., a diameter, a width, or a length, or an effective average particle size) greater than about 50 nm (e.g., from about 50 nm to 300 nm, 50 nm to 100 nm, 50 nm to 150 nm, 50 nm to 200 nm, 50 nm to 250 nm, 75 nm to 100 nm, 75 nm to 150 nm, 75 nm to 200 nm, 75 nm to 250 nm, 75 nm to 300 nm, 100 nm to 150 nm, 100 nm to 200 nm, 100 nm to 250 nm, 100 nm to 300 nm, 125 nm to 150 nm, 125 nm to 200 nm, 125 nm to 250 nm, 125 nm to 300 nm, 150 nm to 200 nm, 150 nm to 250 nm, 150 nm to 300 nm, 175 nm to 200 nm, 175 nm to 250 nm, 175 nm to 300 nm, 200 nm to 250 nm, 200 nm to 300 nm, 225 nm to 250 nm, 225 nm to 300 nm, 250 nm to 300 nm, or 275 nm to 300 nm).

The cargo can be any useful agent, e.g., a CRISPR component, such as any described herein. Exemplary CRISPR components include a Cas protein, a guide nucleic acid, a plasmid, as well as combinations thereof (e.g., a ribonucleoprotein complex). In some embodiments, an average dimension of the pores is greater than a dimension of the cargo. In other embodiments, an average dimension of the pores is smaller than a dimension of the cargo.

In particular embodiments, the construct further includes an outer layer. Exemplary, non-limiting outer layers can include a lipid, a polymer, a moiety (e.g., a targeting ligand), or a combination thereof.

The present invention also relates to uses of the construct, such as formulations thereof, synthetic methods thereof, and methods of use thereof.

Accordingly, in a first aspect, the present invention features a construct including: a core including an external surface and a plurality of pores in fluidic communication with the external surface, wherein an average dimension of the plurality of pores is greater than about 5 nm (e.g., of from about 5 nm to about 50 nm, as well as any ranges described herein); a spacer (e.g., any described herein) disposed within the at least one pore and/or upon the external surface of the core; a cargo attached to the spacer (e.g., by a bond, including a covalent bond, an ionic bond, a coordination bond, or any described herein); and an outer layer disposed upon the external surface of the core, wherein the outer layer includes a lipid, a polymer, or a combination thereof (e.g., any lipid and/or polymer described herein, including one or more of a cationic lipid, a pegylated lipid, a zwitterionic lipid, a sterol (e.g., a cholesterol), a targeting ligand, and/or a polymer).

In some embodiments, the core includes a mesoporous silica nanoparticle. In particular embodiments, the average dimension of the plurality of pores is of from about 5 nm to about 30 nm.

In some embodiments, the spacer includes a covalent bond or a coordination bond (e.g., a bond to a divalent metal or a transition metal) to a functional group present on the cargo. In other embodiments, the functional group includes heteroaryl, imidazolyl, amino, amido, carboxyl, thiol, histidine, lysine, or cysteine. In some embodiments, the spacer includes a cleavable moiety (e.g., any described herein).

In some embodiments, the cargo includes a ribonucleoprotein complex, a protein, a plasmid, a nucleic acid, or a combination thereof. In particular embodiments, the cargo includes a CRISPR component or a nucleic acid sequence encoding a CRISPR component. In yet other embodiments, the cargo includes a sequence having at least 80% sequence identity to any one of SEQ ID NOs:20-32, 40-54, 60-65, 80-93, or 100-103, or a fragment thereof, a complement thereof, or a reverse complement thereof. In other embodiments, the cargo includes a sequence having at least 80% sequence identity to any one of SEQ ID NOs:110-117, or a fragment thereof.

In some embodiments, the cargo includes a nucleic sequence encoding for an amino acid sequence having at least 80% sequence identity to any one of SEQ ID NOs:110-117, or a fragment thereof.

In some embodiments, the outer layer includes a lipid layer (e.g., a lipid bilayer, a lipid monolayer, or a lipid multilayer). In particular embodiments, the lipid layer includes a cationic lipid, a pegylated lipid, a zwitterionic lipid, and/or a cholesterol. In other embodiments, the construct includes one or more moieties provided on an external surface of the outer layer. In some embodiments, the one or more moieties is selected from the group of a targeting ligand.

In a second aspect, the present invention features a formulation including a plurality of constructs (e.g., any described herein) and an optional pharmaceutically acceptable excipient.

In a third aspect, the present invention features a method of treating a subject, the method including: administering an effective amount of a construct (e.g., any described herein) or a formulation (e.g., any described herein) to the subject (e.g., a human subject).

In a fourth aspect, the present invention features a method of transforming a subject, the method including: administering a construct (e.g., any described herein) or a formulation (e.g., any described herein) to the subject (e.g., a human subject), thereby modulating a target sequence of the subject.

In some embodiments, the cargo of the construct or the formulation is configured bind to the target sequence of the subject. In other embodiments, the cargo includes a CRISPR component or a nucleic acid sequence encoding a CRISPR component. In yet other embodiments, the cargo includes a sequence having at least 80% sequence identity to any one of SEQ ID NOs:20-32, 40-54, 60-65, 80-93, or 100-103, or a fragment thereof, a complement thereof, or a reverse complement thereof. In other embodiments, the cargo includes a sequence having at least 80% sequence identity to any one of SEQ ID NOs:110-117, or a fragment thereof.

In some embodiments, the cargo includes a nucleic sequence encoding for an amino acid sequence having at least 80% sequence identity to any one of SEQ ID NOs:110-117, or a fragment thereof.

In a fifth aspect, the present invention features a method of forming a construct, the method including: providing a core including an external surface and a plurality of pores in fluidic communication with the external surface, wherein an average dimension of the plurality of pores is characterized by a first dimension; expanding the pores, thereby providing a core including a plurality of expanded pores, wherein an average dimension of the plurality of expanded pores is characterized by a second dimension that is greater than the first dimension; installing a spacer (e.g., any described herein) to be disposed within the at least one pore and/or upon the external surface of the core; incubating the core with one or more cargo, thereby providing a loaded core, wherein the incubating step can optionally include binding the cargo to the spacer; and exposing the loaded core to a lipid formulation to form an outer layer supported upon the external surface of the core, thereby providing the construct. In some embodiments, the second dimension is of from about 5 nm to about 30 nm.

In other embodiments, the method further includes (e.g., after the expanding step): installing a spacer to be disposed within the at least one pore and/or upon the external surface of the core, wherein the incubating step can optionally include binding the cargo to the spacer.

In some embodiments, the spacer includes a cleavable moiety. In other embodiments, the method further includes exposing the construct or the spacer to a cleaving agent or a cleaving condition configured to release the cargo and/or the core.

Additional details follow.

Definitions

As used herein, the term “about” means+/−10% of any recited value. As used herein, this term modifies any recited value, range of values, or endpoints of one or more ranges.

By “micro” is meant having at least one dimension that is less than 1 mm but equal to or larger than 1 μm. For instance, a microstructure (e.g., any structure described herein, such as a microparticle) can have a length, width, height, cross-sectional dimension, circumference, radius (e.g., external or internal radius), or diameter that is less than 1 mm but equal to or larger than 1 μm. In another instance, the microstructure has a dimension that is of from about 1 μm to 1 mm.

By “nano” is meant having at least one dimension that is less than 1 m but equal to or larger than 1 nm. For instance, a nanostructure (e.g., any structure described herein, such as a nanoparticle) can have a length, width, height, cross-sectional dimension, circumference, radius (e.g., external or internal radius), or diameter that is less than 1 m but equal to or larger than 1 nm. In another instance, the nanostructure has a dimension that is of from about 1 nm to about 1 μm.

The term “cargo” is used herein to describe any molecule or compound, whether a small molecule or macromolecule having an activity relevant to its use in particles (e.g., a construct, a nanoparticle, or a mesoporous silica nanoparticle), especially including biological activity, which can be included in particles according to the present invention. In principal embodiments of the present invention, the cargo is a nucleic acid sequence, such as double stranded (ds) plasmid DNA. The cargo may be included within the pores, associated with the pore (e.g., by way of a spacer), and/or on the surface of the core (e.g., by way of a spacer) according to the present invention. Additional representative cargo may include, for example, a small molecule bioactive agent, a nucleic acid (e.g., RNA or DNA), a polypeptide, including a protein or a carbohydrate. Particular examples of such cargo include RNA, such as mRNA, siRNA, shRNA micro RNA, a polypeptide or protein, including a protein toxin (e.g., ricin toxin A-chain or diphtheria toxin A-chain), and/or DNA (including double stranded or linear DNA, complementary DNA (cDNA), minicircle DNA, naked DNA and plasmid DNA, which optionally may be supercoiled and/or packaged (e.g., with histones) and which may be optionally modified with a nuclear localization sequence). Cargo may also include a reporter as described herein.

The phrase “effective average particle size” as used herein to describe a multiparticulate (e.g., a porous nanoparticulate) means that at least 50% of the particles therein are of a specified size. Accordingly, “effective average particle size of less than about 2,000 nm in diameter” means that at least 50% of the particles therein are less than about 2,000 nm in diameter. In certain embodiments, nanoparticulates have an effective average particle size of less than about 2,000 nm (i.e., 2 microns), less than about 1,900 nm, less than about 1,800 nm, less than about 1,700 nm, less than about 1,600 nm, less than about 1,500 nm, less than about 1,400 nm, less than about 1,300 nm, less than about 1,200 nm, less than about 1,100 nm, less than about 1,000 nm, less than about 900 nm, less than about 800 nm, less than about 700 nm, less than about 600 nm, less than about 500 nm, less than about 400 nm, less than about 300 nm, less than about 250 nm, less than about 200 nm, less than about 150 nm, less than about 100 nm, less than about 75 nm, or less than about 50 nm, as measured by light-scattering methods, microscopy, or other appropriate methods. In certain aspects of the present invention, the particles are monodisperse and generally no greater than about 50 nm in average diameter, often less than about 30 nm in average diameter, as otherwise described herein. The term “D₅₀” refers to the particle size below which 50% of the particles in a multiparticulate fall. Similarly, the term “D₉₀” refers to the particle size below which 90% of the particles in a multiparticulate fall.

The term “monodisperse” is used as a standard definition established by the National Institute of Standards and Technology (NIST) (Particle Size Characterization, Special Publication 960-1, January 2001) to describe a distribution of particle size within a population of particles, in this case nanoparticles, which particle distribution may be considered monodisperse if at least 90% of the distribution lies within 5% of the median size. See, e.g., Takeuchi S et al., Adv. Mater. 2005; 17(8):1067-72.

The term “lipid” is used to describe the components which are used to form lipid mono-, bi-, or multilayers on the surface of the particles (e.g., a core of the particle), that are used in the present invention (e.g., as constructs) and may include a PEGylated lipid. Various embodiments provide nanostructures, that are constructed from nanoparticles, which support one or more lipid layers (e.g., bilayer(s) or multilayer(s)). In embodiments according to the present invention, the nanostructures preferably include, for example, a core-shell structure including a porous particle core surrounded by a shell of one or more lipid bilayer(s). In one non-limiting embodiment, the nanostructure (e.g., a porous silica or alum nanostructure) supports the lipid bilayer membrane structure.

The terms “targeting ligand” and “targeting active species” are used to describe a compound or moiety (e.g., an antigen), which is complexed or covalently bonded to the surface of particle according to the present invention (e.g., either directly on an outer surface of a delivery platform or on an outer layer). The targeting ligand, in turn, binds to a moiety on the surface of a cell to be targeted so that the constructs may bind to the surface of the targeted cell, enter the cell or an organelle thereof, and/or deposit their contents into the cell. The targeting active species for use in the present invention is preferably a targeting peptide (e.g., a receptor ligand, a cell penetration peptide, a fusogenic peptide, or an endosomolytic peptide, as otherwise described herein), a polypeptide including an antibody or antibody fragment, an aptamer, or a carbohydrate, among other species that bind (e.g., selectively bind) to a targeted cell.

The term “reporter” is used to describe an imaging agent or moiety which is incorporated into the outer layer or cargo of particles according to an embodiment of the present invention and provides a signal that can be measured. The moiety may provide a fluorescent signal or may be a radioisotope which allows radiation detection, among others. Exemplary fluorescent labels for use in particles (preferably via conjugation or adsorption to the outer layer or the core, via integration into the matrix of the core, and/or via incorporation into cargo elements such as DNA, RNA, polypeptides and small molecules which are delivered to cells by the particles) include Hoechst 33342 (350/461), 4′,6-diamidino-2-phenylindole (DAPI, 356/451), Alexa Fluor® 405 carboxylic acid, succinimidyl ester (401/421), CellTracker™ Violet BMQC (415/516), CellTracker™ Green CMFDA (492/517), CellTracker™ Blue CMAC (353/466), CellTracker™ Blue CMF₂HC (371/464), CellTracker™ Blue CMHC (372/470), calcein (495/515), Alexa Fluor® 488 conjugate of annexin V (495/519), Alexa Fluor® 488 goat anti-mouse IgG (H+L) (495/519), Click-iT® AHA Alexa Fluor® 488 Protein Synthesis HCS Assay (495/519), LIVEDEAD® Fixable Green Dead Cell Stain Kit (495/519), SYTOX® Green nucleic acid stain (504/523), MitoSOX™ Red mitochondrial superoxide indicator (510/580), Alexa Fluor® 532 carboxylic acid, succinimidyl ester(532/554), pHrodo™ succinimidyl ester (558/576), CellTracker™ Red CMTPX (577/602), Texas Red® 1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine (Texas Red® DHPE, 583/608), Alexa Fluor® 647 hydrazide (649/666), Alexa Fluor® 647 carboxylic acid, succinimidyl ester (650/668), Ulysis™ Alexa Fluor® 647 Nucleic Acid Labeling Kit (650/670), Alexa Fluor® 647 conjugate of annexin V (650/665), other fluorescent labels, colorimetric labels, quantum dots, nanoparticles, microparticles, barcodes, radio labels (e.g., RF labels or barcodes), avidin, biotin, tags, dyes, an enzyme that can optionally include one or more linking agents and/or one or more dyes, as well as combinations thereof etc. Additional reports can include a detection agent (e.g., a dye, such as an electroactive detection agent, a fluorescent dye, a luminescent dye, a chemiluminescent dye, a colorimetric dye, a radioactive agent, a contrast agent, etc.), a particle (e.g., such as a microparticle, a nanoparticle, a latex bead, a colloidal particle, a magnetic particle, a fluorescent particle, etc.), and/or a label (e.g., an electroactive label, an electrocatalytic label, a fluorescent label, a colorimetric label, a quantum dot, a nanoparticle, a microparticle, a barcode, a radio label (e.g., an RF label or barcode), avidin, biotin, a tag, a dye, a marker, an enzyme that can optionally include one or more linking agents and/or one or more dyes). Moieties that enhance the fluorescent signal or slow the fluorescent fading may also be incorporated and include SlowFade® Gold antifade reagent (with and without DAPI) and Image-iT® FX signal enhancer. All of these are well known in the art.

The terms “polynucleotide” and “nucleic acid,” used interchangeably herein, refer to a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides. Thus, this term includes, but is not limited to, single-stranded (e.g., sense or antisense), double-stranded, or multi-stranded ribonucleic acids (RNAs), deoxyribonucleic acids (DNAs), threose nucleic acids (TNAs), glycol nucleic acids (GNAs), peptide nucleic acids (PNAs), locked nucleic acids (LNAs), or hybrids thereof, genomic DNA, cDNA, DNA-RNA hybrids, or a polymer comprising purine and pyrimidine bases or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases. Polynucleotides can have any useful two-dimensional or three-dimensional structure or motif, such as regions including one or more duplex, triplex, quadruplex, hairpin, and/or pseudoknot structures or motifs. In any nucleic acid described herein, U may be replaced with T and vice versa.

The term “modified,” as used in reference to nucleic acids, means a nucleic acid sequence including one or more modifications to the nucleobase, nucleoside, nucleotide, phosphate group, sugar group, and/or internucleoside linkage (e.g., phosphodiester backbone, linking phosphate, or a phosphodiester linkage).

The nucleoside modification may include, but is not limited to, pyridin-4-one ribonucleoside, 5-aza-uridine, 2-thio-5-aza-uridine, 2-thiouridine, 4-thio-pseudouridine, 2-thio-pseudouridine, 5-hydroxyuridine, 3-methyluridine, 5-carboxymethyl-uridine, 1-carboxymethyl-pseudouridine, 5-propynyl-uridine, 1-propynyl-pseudouridine, 5-taurinomethyluridine, 1-taurinomethyl-pseudouridine, 5-taurinomethyl-2-thio-uridine, 1-taurinomethyl-4-thio-uridine, 5-methyl-uridine, 1-methyl-pseudouridine, 4-thio-1-methyl-pseudouridine, 2-thio-1-methyl-pseudouridine, 1-methyl-1-deaza-pseudouridine, 2-thio-1-methyl-1-deaza-pseudouridine, dihydrouridine, dihydropseudouridine, 2-thio-dihydrouridine, 2-thio-dihydropseudouridine, 2-methoxyuridine, 2-methoxy-4-thio-uridine, 4-methoxy-pseudouridine, 4-methoxy-2-thio-pseudouridine, 5-aza-cytidine, pseudoisocytidine, 3-methyl-cytidine, N4-acetylcytidine, 5-formylcytidine, N4-methylcytidine, 5-hydroxymethylcytidine, 1-methyl-pseudoisocytidine, pyrrolo-cytidine, pyrrolo-pseudoisocytidine, 2-thio-cytidine, 2-thio-5-methyl-cytidine, 4-thio-pseudoisocytidine, 4-thio-1-methyl-pseudoisocytidine, 4-thio-1-methyl-1-deaza-pseudoisocytidine, 1-methyl-1-deaza-pseudoisocytidine, zebularine, 5-aza-zebularine, 5-methyl-zebularine, 5-aza-2-thio-zebularine, 2-thio-zebularine, 2-methoxy-cytidine, 2-methoxy-5-methyl-cytidine, 4-methoxy-pseudoisocytidine, 4-methoxy-1-methyl-pseudoisocytidine, 2-aminopurine, 2,6-diaminopurine, 7-deaza-adenine, 7-deaza-8-aza-adenine, 7-deaza-2-aminopurine, 7-deaza-8-aza-2-aminopurine, 7-deaza-2,6-diaminopurine, 7-deaza-8-aza-2,6-diaminopurine, 1-methyladenosine, N6-methyladenosine, N6-isopentenyladenosine, N6-(cis-hydroxyisopentenyl)adenosine, 2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine, N6-glycinylcarbamoyladenosine, N6-threonylcarbamoyladenosine, 2-methylthio-N6-threonyl carbamoyladenosine, N6,N6-dimethyladenosine, 7-methyladenine, 2-methylthio-adenine, and 2-methoxy-adenine, inosine, 1-methyl-inosine, wyosine, wybutosine, 7-deaza-guanosine, 7-deaza-8-aza-guanosine, 6-thio-guanosine, 6-thio-7-deaza-guanosine, 6-thio-7-deaza-8-aza-guanosine, 7-methyl-guanosine, 6-thio-7-methyl-guanosine, 7-methylinosine, 6-methoxy-guanosine, 1-methylguanosine, N2-methylguanosine, N2,N2-dimethylguanosine, 8-oxo-guanosine, 7-methyl-8-oxo-guanosine, 1-methyl-6-thio-guanosine, N2-methyl-6-thio-guanosine, and N2,N2-dimethyl-6-thio-guanosine, and combinations thereof.

A sugar modification may include, but is not limited to, a locked nucleic acid (LNA, in which the 2′-hydroxyl is connected by a C₁₋₆ alkylene or C₁₋₆ heteroalkylene bridge to the 4′-carbon of the same ribose sugar), replacement of the oxygen in ribose (e.g., with S, Se, or alkylene, such as methylene or ethylene), addition of a double bond (e.g., to replace ribose with cyclopentenyl or cyclohexenyl), ring contraction of ribose (e.g., to form a 4-membered ring of cyclobutane or oxetane), ring expansion of ribose (e.g., to form a 6- or 7-membered ring having an additional carbon or heteroatom, such as for anhydrohexitol, altritol, mannitol, cyclohexanyl, cyclohexenyl, and morpholino that also has a phosphoramidate backbone), multicyclic forms (e.g., tricyclic), and “unlocked” forms, such as glycol nucleic acid (GNA) (e.g., R-GNA or S-GNA, where ribose is replaced by glycol units attached to phosphodiester bonds), threose nucleic acid (TNA, where ribose is replace with a-L-threofuranosyl-(3′→2′)), and peptide nucleic acid (PNA, where 2-amino-ethyl-glycine linkages replace the ribose and phosphodiester backbone). The sugar group can also contain one or more carbons that possess the opposite stereochemical configuration than that of the corresponding carbon in ribose. Thus, a polynucleotide molecule can include nucleotides containing, e.g., arabinose, as the sugar.

A backbone modification may include, but is not limited to, 2′-deoxy- or 2′-O-methyl modifications. A phosphate group modification may include, but is not limited to, phosphorothioate, phosphoroselenates, boranophosphates, boranophosphate esters, hydrogen phosphonates, phosphoramidates, phosphorodiamidates, alkyl or aryl phosphonates, phosphotriesters, phosphorodithioates, bridged phosphoramidates, bridged phosphorothioates, or bridged methylene-phosphonates.

“Complementarity” or “complementary” refers to the ability of a nucleic acid to form hydrogen bond(s) with another nucleic acid sequence by either traditional Watson-Crick or other non-traditional types, e.g., form Watson-Crick base pairs and/or G/U base pairs, “anneal”, or “hybridize,” to another nucleic acid in a sequence-specific, antiparallel, manner (i.e., a nucleic acid specifically binds to a complementary nucleic acid) under the appropriate in vitro and/or in vivo conditions of temperature and solution ionic strength. As is known in the art, standard Watson-Crick base-pairing includes: adenine (A) pairing with thymidine (T), adenine (A) pairing with uracil (U), and guanine (G) pairing with cytosine (C). In addition, it is also known in the art that for hybridization between two RNA molecules (e.g., dsRNA), guanine (G) base pairs with uracil (U). A percent complementarity indicates the percentage of residues in a nucleic acid molecule which can form hydrogen bonds (e.g., Watson-Crick base pairing) with a second nucleic acid sequence (e.g., 5, 6, 7, 8, 9, 10 out of 10 being 50%, 60%, 70%, 80%, 90%, and 100% complementary). “Perfectly complementary” means that all the contiguous residues of a nucleic acid sequence will hydrogen bond with the same number of contiguous residues in a second nucleic acid sequence. “Substantially complementary” or “sufficient complementarity” as used herein refers to a degree of complementarity that is at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%. 97%, 98%, 99%, or 100% over a region of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, or more nucleotides, or refers to two nucleic acids that hybridize under stringent conditions.

As used herein, “stringent conditions” for hybridization refer to conditions under which a nucleic acid having complementarity to a target sequence predominantly hybridizes with the target sequence, and substantially does not hybridize to non-target sequences. Stringent conditions are generally sequence-dependent, and vary depending on a number of factors. In general, the longer the sequence, the higher the temperature at which the sequence specifically hybridizes to its target sequence. Non-limiting examples of stringent conditions are described in detail in Tijssen (1993), Laboratory Techniques In Biochemistry And Molecular Biology-Hybridization With Nucleic Acid Probes Part 1, Second Chapter “Overview of principles of hybridization and the strategy of nucleic acid probe assay”, Elsevier, N.Y.

“Hybridization” refers to a reaction in which one or more polynucleotides react to form a complex that is stabilized via hydrogen bonding between the bases of the nucleotide residues. The hydrogen bonding may occur by Watson Crick base pairing, Hoogstein binding, or in any other sequence specific manner. The complex may comprise two strands forming a duplex structure, three or more strands forming a multi stranded complex, a single self-hybridizing strand, or any combination of these. A hybridization reaction may constitute a step in a more extensive process, such as the initiation of PCR, or the cleavage of a polynucleotide by an enzyme. A sequence capable of hybridizing with a given sequence is referred to as the “complement” of the given sequence. Hybridization and washing conditions are well known and exemplified in Sambrook J, Fritsch E F, and Maniatis T, “Molecular Cloning: A Laboratory Manual,” Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (1989), particularly Chapter 11 and Table 11.1 therein; and Sambrook J and Russell W, “Molecular Cloning: A Laboratory Manual,” Third Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (2001). The conditions of temperature and ionic strength determine the “stringency” of the hybridization.

Hybridization requires that the two nucleic acids contain complementary sequences, although mismatches between bases are possible. The conditions appropriate for hybridization between two nucleic acids depend on the length of the nucleic acids and the degree of complementation, variables well known in the art. The greater the degree of complementation between two nucleotide sequences, the greater the value of the melting temperature (Tm) for hybrids of nucleic acids having those sequences. For hybridizations between nucleic acids with short stretches of complementarity (e.g., complementarity over 35 or less, 30 or less, 25 or less, 22 or less, 20 or less, or 18 or less nucleotides) the position of mismatches becomes important (see Sambrook et al., supra, 11.7-11.8). Typically, the length for a hybridizable nucleic acid is at least about 10 nucleotides. Illustrative minimum lengths for a hybridizable nucleic acid are: at least about 15 nucleotides; at least about 20 nucleotides; at least about 22 nucleotides; at least about 25 nucleotides; and at least about 30 nucleotides). Furthermore, the skilled artisan will recognize that the temperature and wash solution salt concentration may be adjusted as necessary, according to factors such as length of the region of complementation and the degree of complementation.

It is understood in the art that the sequence of polynucleotide need not be 100% complementary to that of its target nucleic acid to be specifically hybridizable or hybridizable. Moreover, a polynucleotide may hybridize over one or more segments such that intervening or adjacent segments are not involved in the hybridization event (e.g., a loop structure or hairpin structure). A polynucleotide can comprise at least 70%, at least 80%, at least 90%, at least 95%, at least 99%, or 100% sequence complementarity to a target region within the target nucleic acid sequence to which they are targeted. For example, an antisense nucleic acid in which 18 of 20 nucleotides of the antisense compound are complementary to a target region, and would therefore specifically hybridize, would represent 90 percent complementarity. In this example, the remaining noncomplementary nucleotides may be clustered or interspersed with complementary nucleotides and need not be contiguous to each other or to complementary nucleotides. Percent complementarity between particular stretches of nucleic acid sequences within nucleic acids can be determined routinely using BLAST programs (basic local alignment search tools) and PowerBLAST programs known in the art (Altschul S F et al., J. Mol. Biol. 1990; 215:403-10; Zhang J et al., Genome Res. 1997; 7:649-56) or by using the Gap program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, Madison Wis.), using default settings, which uses the algorithm of Smith T F et al., Adv. Appl. Math. 1981; 2(4):482-9).

By “protein,” “peptide,” or “polypeptide,” as used interchangeably, is meant any chain of more than two amino acids, regardless of post-translational modification (e.g., glycosylation or phosphorylation), constituting all or part of a naturally occurring polypeptide or peptide, or constituting a non-naturally occurring polypeptide or peptide, which can include coded amino acids, non-coded amino acids, modified amino acids (e.g., chemically and/or biologically modified amino acids), and/or modified backbones.

The term “fragment” is meant a portion of a nucleic acid or a polypeptide that is at least one nucleotide or one amino acid shorter than the reference sequence. This portion contains, preferably, at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% of the entire length of the reference nucleic acid molecule or polypeptide. A fragment may contain 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 1800 or more nucleotides; or 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 640 amino acids or more. In another example, any polypeptide fragment can include a stretch of at least about 5 (e.g., about 10, about 20, about 30, about 40, about 50, or about 100) amino acids that are at least about 40% (e.g., about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, about 87%, about 98%, about 99%, or about 100%) identical to any of the sequences described herein can be utilized in accordance with the invention. In certain embodiments, a polypeptide to be utilized in accordance with the invention includes 2, 3, 4, 5, 6, 7, 8, 9, 10, or more mutations (e.g., one or more conservative amino acid substitutions, as described herein). In yet another example, any nucleic acid fragment can include a stretch of at least about 5 (e.g., about 7, about 8, about 10, about 12, about 14, about 18, about 20, about 24, about 28, about 30, or more) nucleotides that are at least about 40% (about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, about 87%, about 98%, about 99%, or about 100%) identical to any of the sequences described herein can be utilized in accordance with the invention.

The term “conservative amino acid substitution” refers to the interchangeability in proteins of amino acid residues having similar side chains (e.g., of similar size, charge, and/or polarity). For example, a group of amino acids having aliphatic side chains consists of glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains consists of serine and threonine; a group of amino acids having amide containing side chains consisting of asparagine and glutamine; a group of amino acids having aromatic side chains consists of phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains consists of lysine, arginine, and histidine; a group of amino acids having acidic side chains consists of glutamic acid and aspartic acid; and a group of amino acids having sulfur containing side chains consists of cysteine and methionine. Exemplary conservative amino acid substitution groups are valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, glycine-serine, glutamate-aspartate, and asparagine-glutamine.

As used herein, when a polypeptide or nucleic acid sequence is referred to as having “at least X % sequence identity” to a reference sequence, it is meant that at least X percent of the amino acids or nucleotides in the polypeptide or nucleic acid are identical to those of the reference sequence when the sequences are optimally aligned. An optimal alignment of sequences can be determined in various ways that are within the skill in the art, for instance, the Smith Waterman alignment algorithm (Smith T F et al., J. Mol. Biol. 1981; 147:195-7) and BLAST (Basic Local Alignment Search Tool; Altschul S F et al., J. Mol. Biol. 1990; 215:403-10). These and other alignment algorithms are accessible using publicly available computer software such as “Best Fit” (Smith T F et al., Adv. Appl. Math. 1981; 2(4):482-9) as incorporated into GeneMatcher Plus™ (Schwarz and Dayhof, “Atlas of Protein Sequence and Structure,” ed. Dayhoff, M. O., pp. 353-358, 1979), BLAST, BLAST-2, BLAST-P, BLAST-N, BLAST-X, WU-BLAST-2, ALIGN, ALIGN-2, CLUSTAL, T-COFFEE, MUSCLE, MAFFT, or Megalign (DNASTAR). In addition, those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve optimal alignment over the length of the sequences being compared. In general, for polypeptides, the length of comparison sequences can be at least five amino acids, preferably 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 125, 150, 175, 200, 250, 300, 400, 500, 600, 700, or more amino acids, up to the entire length of the polypeptide. For nucleic acids, the length of comparison sequences can generally be at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 125, 150, 175, 200, 250, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, or more nucleotides, up to the entire length of the nucleic acid molecule. It is understood that for the purposes of determining sequence identity when comparing a DNA sequence to an RNA sequence, a thymine nucleotide is equivalent to an uracil nucleotide.

By “substantial identity” or “substantially identical” is meant a polypeptide or nucleic acid sequence that has the same polypeptide or nucleic acid sequence, respectively, as a reference sequence, or has a specified percentage of amino acid residues or nucleotides, respectively, that are the same at the corresponding location within a reference sequence when the two sequences are optimally aligned. For example, an amino acid sequence that is “substantially identical” to a reference sequence has at least about 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the reference amino acid sequence. For polypeptides, the length of comparison sequences will generally be at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 50, 75, 90, 100, 150, 200, 250, 300, or 350 contiguous amino acids (e.g., a full-length sequence). For nucleic acids, the length of comparison sequences will generally be at least 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 contiguous nucleotides (e.g., the full-length nucleotide sequence). Sequence identity may be measured using sequence analysis software on the default setting (e.g., Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis., 53705). Such software may match similar sequences by assigning degrees of homology to various substitutions, deletions, and other modifications.

The term “chimeric” as used herein as applied to a nucleic acid or polypeptide refers to two components that are defined by structures derived from different sources. For example, where “chimeric” is used in the context of a chimeric polypeptide (e.g., a chimeric Cas9/Csn1 protein), the chimeric polypeptide includes amino acid sequences that are derived from different polypeptides. A chimeric polypeptide may comprise either modified or naturally-occurring polypeptide sequences (e.g., a first amino acid sequence from a modified or unmodified Cas9/Csn1 protein; and a second amino acid sequence other than the Cas9/Csn1 protein). Similarly, “chimeric” in the context of a polynucleotide encoding a chimeric polypeptide includes nucleotide sequences derived from different coding regions (e.g., a first nucleotide sequence encoding a modified or unmodified Cas9/Csn1 protein; and a second nucleotide sequence encoding a polypeptide other than a Cas9/Csn1 protein).

The term “chimeric polypeptide” refers to a polypeptide which is made by the combination (i.e., “fusion”) of two otherwise separated segments of amino sequence, usually through human intervention. A polypeptide that comprises a chimeric amino acid sequence is a chimeric polypeptide. Some chimeric polypeptides can be referred to as “fusion variants.”

“Heterologous,” as used herein, means a nucleotide or polypeptide sequence that is not found in the native nucleic acid or protein, respectively. For example, in a chimeric Cas9/Csn1 protein, the RNA-binding domain of a naturally-occurring bacterial Cas9/Csn1 polypeptide (or a variant thereof) may be fused to a heterologous polypeptide sequence (i.e., a polypeptide sequence from a protein other than Cas9/Csn1 or a polypeptide sequence from another organism). The heterologous polypeptide sequence may exhibit an activity (e.g., enzymatic activity) that will also be exhibited by the chimeric Cas9/Csn1 protein (e.g., methyltransferase activity, acetyltransferase activity, kinase activity, ubiquitinating activity, etc.). A heterologous nucleic acid sequence may be linked to a naturally-occurring nucleic acid sequence (or a variant thereof) (e.g., by genetic engineering) to generate a chimeric nucleotide sequence encoding a chimeric polypeptide. As another example, in a fusion variant Cas9 site-directed polypeptide, a variant Cas9 site-directed polypeptide may be fused to a heterologous polypeptide (i.e., a polypeptide other than Cas9), which exhibits an activity that will also be exhibited by the fusion variant Cas9 site-directed polypeptide. A heterologous nucleic acid sequence may be linked to a variant Cas9 site-directed polypeptide (e.g., by genetic engineering) to generate a nucleotide sequence encoding a fusion variant Cas9 site-directed polypeptide.

“Recombinant,” as used herein, means that a particular nucleic acid, as defined herein, is the product of various combinations of cloning, restriction, polymerase chain reaction (PCR) and/or ligation steps resulting in a construct having a structural coding or non-coding sequence distinguishable from endogenous nucleic acids found in natural systems. DNA sequences encoding polypeptides can be assembled from cDNA fragments or from a series of synthetic oligonucleotides, to provide a synthetic nucleic acid which is capable of being expressed from a recombinant transcriptional unit contained in a cell or in a cell-free transcription and translation system. Genomic DNA comprising the relevant sequences can also be used in the formation of a recombinant gene or transcriptional unit. Sequences of non-translated DNA may be present 5′ or 3′ from the open reading frame, where such sequences do not interfere with manipulation or expression of the coding regions, and may indeed act to modulate production of a desired product by various mechanisms. Alternatively, DNA sequences encoding RNA (e.g., DNA-targeting RNA) that is not translated may also be considered recombinant. Thus, e.g., the term “recombinant” nucleic acid refers to one which is not naturally occurring, e.g., is made by the artificial combination of two otherwise separated segments of sequence through human intervention. This artificial combination is often accomplished by either chemical synthesis means, or by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques. Such is usually done to replace a codon with a codon encoding the same amino acid, a conservative amino acid, or a non-conservative amino acid. Alternatively, it is performed to join together nucleic acid segments of desired functions to generate a desired combination of functions. This artificial combination is often accomplished by either chemical synthesis means, or by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques. When a recombinant polynucleotide encodes a polypeptide, the sequence of the encoded polypeptide can be naturally occurring (“wild type”) or can be a variant (e.g., a mutant) of the naturally occurring sequence. Thus, the term “recombinant” polypeptide does not necessarily refer to a polypeptide whose sequence does not naturally occur. Instead, a “recombinant” polypeptide is encoded by a recombinant DNA sequence, but the sequence of the polypeptide can be naturally occurring (“wild type”) or non-naturally occurring (e.g., a variant, a mutant, etc.). Thus, a “recombinant” polypeptide is the result of human intervention, but may be a naturally occurring amino acid sequence.

A “target sequence” as used herein is a polynucleotide (e.g., as defined herein, including a DNA, RNA, or DNA/RNA hybrid, as well as modified forms thereof) that includes a “target site.” The terms “target site” or “target protospacer DNA” are used interchangeably herein to refer to a nucleic acid sequence present in a target genomic sequence (e.g., DNA or RNA in a host cell) to which a targeting portion of the guiding component will bind provided sufficient conditions (e.g., sufficient complementarity) for binding exist. Suitable DNA/RNA binding conditions include physiological conditions normally present in a cell. Other suitable DNA/RNA binding conditions (e.g., conditions in a cell-free system) are known in the art; see, e.g., Sambrook, supra.

By “cleavage” it is meant the breakage of the covalent backbone of a target sequence (e.g., a nucleic acid molecule). Cleavage can be initiated by a variety of methods including, but not limited to, enzymatic or chemical hydrolysis of a phosphodiester bond. Both single-stranded cleavage and double-stranded cleavage are possible, and double-stranded cleavage can occur as a result of two distinct single-stranded cleavage events. DNA cleavage can result in the production of either blunt ends or staggered ends. In certain embodiments, a complex comprising a guiding component and a nuclease is used for targeted double-stranded DNA cleavage. In other embodiments, a complex comprising a guiding component and a nuclease is used for targeted single-stranded RNA cleavage.

“Nuclease” and “endonuclease” are used interchangeably herein to mean an enzyme which possesses catalytic activity for DNA cleavage and/or RNA cleavage.

By “cleavage domain” or “active domain” or “nuclease domain” of a nuclease it is meant the polypeptide sequence or domain within the nuclease which possesses the catalytic activity for nucleic acid cleavage. A cleavage domain can be contained in a single polypeptide chain or cleavage activity can result from the association of two (or more) polypeptides. A single nuclease domain may consist of more than one isolated stretch of amino acids within a given polypeptide.

A “host cell,” as used herein, denotes an in vivo or in vitro eukaryotic cell, a prokaryotic cell (e.g., bacterial or archaeal cell), or a cell from a multicellular organism (e.g., a cell line) cultured as a unicellular entity, which eukaryotic or prokaryotic cells can be, or have been, used as recipients for a nucleic acid, and include the progeny of the original cell which has been transformed by the nucleic acid. It is understood that the progeny of a single cell may not necessarily be completely identical in morphology or in genomic or total DNA complement as the original parent, due to natural, accidental, or deliberate mutation. A “recombinant host cell” (also referred to as a “genetically modified host cell”) is a host cell into which has been introduced a heterologous nucleic acid, e.g., an expression vector. For example, a subject bacterial host cell is a genetically modified bacterial host cell by virtue of introduction into a suitable bacterial host cell of an exogenous nucleic acid (e.g., a plasmid or recombinant expression vector) and a subject eukaryotic host cell is a genetically modified eukaryotic host cell (e.g., a mammalian germ cell), by virtue of introduction into a suitable eukaryotic host cell of an exogenous nucleic acid.

By “linker” or “spacer”, unless otherwise indicated, is meant any useful multivalent (e.g., bivalent) component useful for joining to different portions or segments. Exemplary linkers and spacers include a nucleic acid sequence, a chemical linker, etc. In one instance, the linker of the guiding component (e.g., linker L in the interacting portion of the guiding component) can have a length of from about 3 nucleotides to about 100 nucleotides. For example, the linker can have a length of from about 3 nucleotides (nt) to about 90 nt, from about 3 nucleotides (nt) to about 80 nt, from about 3 nucleotides (nt) to about 70 nt, from about 3 nucleotides (nt) to about 60 nt, from about 3 nucleotides (nt) to about 50 nt, from about 3 nucleotides (nt) to about 40 nt, from about 3 nucleotides (nt) to about 30 nt, from about 3 nucleotides (nt) to about 20 nt or from about 3 nucleotides (nt) to about 10 nt. For example, the linker can have a length of from about 3 nt to about 5 nt, from about 5 nt to about 10 nt, from about 10 nt to about 15 nt, from about 15 nt to about 20 nt, from about 20 nt to about 25 nt, from about 25 nt to about 30 nt, from about 30 nt to about 35 nt, from about 35 nt to about 40 nt, from about 40 nt to about 50 nt, from about 50 nt to about 60 nt, from about 60 nt to about 70 nt, from about 70 nt to about 80 nt, from about 80 nt to about 90 nt, or from about 90 nt to about 100 nt. In some embodiments, the linker of a single-molecule guiding component is 4 nt.

The term “histone-packaged supercoiled plasmid DNA” is used to describe a component of particles according to the present invention that employ a plasmid DNA that has been “supercoiled” (i.e., folded in on itself using a supersaturated salt solution or other ionic solution which causes the plasmid to fold in on itself and “supercoil” in order to become more dense for efficient packaging into the particles). The plasmid may be virtually any plasmid that expresses any number of polypeptides or encode RNA, including small hairpin RNA/shRNA or small interfering RNA/siRNA, as otherwise described herein. Once supercoiled (using the concentrated salt or other anionic solution), the supercoiled plasmid DNA is then complexed with histone proteins to produce a histone-packaged “complexed” supercoiled plasmid DNA.

“Packaged” DNA herein refers to DNA that is loaded into particles (e.g., adsorbed into the pores, confined directly within the core itself, or confined partially within a pore). To minimize the DNA spatially, it is often packaged, which can be accomplished in several different ways, from adjusting the charge of the surrounding medium to creation of small complexes of the DNA with, for example, lipids, proteins, or other nanoparticles (usually, although not exclusively cationic). Packaged DNA is often achieved via lipoplexes (i.e., complexing DNA with cationic lipid mixtures). In addition, DNA has also been packaged with cationic proteins (including proteins other than histones), as well as gold nanoparticles (e.g., NanoFlares- an engineered DNA and metal complex in which the core of the nanoparticle is gold).

Any number of histone proteins, as well as other means to package the DNA into a smaller volume such as normally cationic nanoparticles, lipids, or proteins, may be used to package the supercoiled plasmid DNA “histone-packaged supercoiled plasmid DNA.” In certain aspects of the invention, a combination of histone proteins H1, H2A, H2B, H3, and H4 in a preferred ratio of 1:2:2:2:2, although other histone proteins may be used in other, similar ratios, as is known in the art or may be readily practiced pursuant to the teachings of the present invention. The DNA may also be double stranded linear DNA, instead of plasmid DNA, which also may be optionally supercoiled and/or packaged with histones or other packaging components.

Other histone proteins which may be used in this aspect of the invention include, for example, H1F, H1A, H1B, H2A, H2B, H1F0, H1FNT, H1FOO, H1FX, H1H1, HIST1H1A, HIST1H1B, HIST1H1C, HIST1H1D, HIST1HE, HIST1H1T, H2AF, H2AFB1, H2AFB2, H2AFB3, H2AFJ, H2AFV, H2AFX, H2AFY, H2AFY2, H2AFZ, H2A1, HIST1H2AA, HIST1H2AB, HIST1H2AC, HIST1H2AD, HIST1H2AE, HIST1H2AG, HIST1H2AI, HIST1H2AJ, HIST1H2AK, HIST1H2AL, HIST1H2AM, H2A2, HIST2H2AA3, HIST2H2AC, H2BF, H2BFM, HSBFS, HSBFWT, H2B1, HIST1H2BA, HIST1HSBB, HIST1HSBC, HIST1HSBD, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BH, HIST1H2BI, HIST1H2BJ, HIST1H2BK, HIST1H2BL, HIST1H2BM, HIST1H2BN, HIST1H2BO, H2B2, HIST2H2BE, H3A1, HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J, H3A2, HIST2H3C, H3A3, HIST3H3, H41, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4G, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, H44, and HIST4H4.

The term “nuclear localization sequence” refers to a peptide sequence incorporated or otherwise crosslinked into histone proteins, which comprise the histone-packaged supercoiled plasmid DNA. In certain embodiments, particles according to the present invention may further comprise a plasmid (often a histone-packaged supercoiled plasmid DNA) which is modified (crosslinked) with a nuclear localization sequence (note that the histone proteins may be crosslinked with the nuclear localization sequence or the plasmid itself can be modified to express a nuclear localization sequence), which enhances the ability of the histone-packaged plasmid to penetrate the nucleus of a cell and deposit its contents there (to facilitate expression and ultimately cell death. These peptide sequences assist in carrying the histone-packaged plasmid DNA and the associated histones into the nucleus of a targeted cell, whereupon the plasmid will express peptides and/or nucleotides as desired to deliver therapeutic and/or diagnostic molecules (polypeptide and/or nucleotide) into the nucleus of the targeted cell. Any number of crosslinking agents, well known in the art, may be used to covalently link a nuclear localization sequence to a histone protein (often at a lysine group or other group which has a nucleophilic or electrophilic group in the side chain of the amino acid exposed pendant to the polypeptide), which can be used to introduce the histone packaged plasmid into the nucleus of a cell. Alternatively, a nucleotide sequence that expresses the nuclear localization sequence can be positioned in a plasmid in proximity to that which expresses histone protein, such that the expression of the histone protein conjugated to the nuclear localization sequence will occur thus facilitating transfer of a plasmid into the nucleus of a targeted cell.

The terms “nucleic acid regulatory sequences,” “control elements,” and “regulatory elements,” used interchangeably herein, refer to transcriptional and translational control sequences, such as promoters, enhancers, polyadenylation signals, internal ribosomal entry sites (IRES), terminators, protein degradation signals, and the like, that provide for and/or regulate transcription of a non-coding sequence (e.g., DNA-targeting RNA) or a coding sequence (e.g., site-directed modifying polypeptide, or Cas9/Csn1 polypeptide) and/or regulate translation of an encoded polypeptide.

A “promoter sequence” is a DNA regulatory region capable of binding RNA polymerase in a cell and initiating transcription of a downstream (3′ direction) coding sequence. For purposes of defining the present invention, the promoter sequence is bounded at its 3′ terminus by the transcription initiation site and extends upstream (5′ direction) to include the minimum number of bases or elements necessary to initiate transcription at levels detectable above background. Within the promoter sequence will be found a transcription initiation, as well as protein binding domains (consensus sequences) responsible for the binding of RNA polymerase. Eukaryotic promoters will often, but not always, contain “TATA” boxes and “CAT” boxes. Prokaryotic promoters contain Shine-Dalgarno sequences in addition to the −10 and −35 consensus sequences.

An “expression control sequence” is a DNA sequence that controls and regulates the transcription and translation of another DNA sequence. A coding sequence is “under the control” of transcriptional and translational control sequences in a cell when RNA polymerase transcribes the coding sequence into mRNA, which is then translated into the protein encoded by the coding sequence. Transcriptional and translational control sequences are DNA regulatory sequences, such as promoters, enhancers, polyadenylation signals, terminators, and the like, that provide for the expression of a coding sequence in a host cell.

A “vector” or “expression vector” is a replicon, such as plasmid, phage, virus, or cosmid, to which another nucleic acid segment, i.e., an “insert”, may be attached so as to bring about the replication of the attached segment in a cell.

An “expression cassette” comprises a nucleic acid coding sequence operably linked, as defined herein, to a promoter sequence, as defined herein.

A “signal sequence” can be included before the coding sequence. This sequence encodes a signal peptide, N-terminal to the polypeptide, that communicates to the host cell to direct the polypeptide to the cell surface or secrete the polypeptide into the media, and this signal peptide is clipped off by the host cell before the protein leaves the cell. Signal sequences can be found associated with a variety of proteins native to prokaryotes and eukaryotes.

“Operably linked” or “operatively linked” or “operatively associated with,” as used interchangeably, refers to a juxtaposition wherein the components so described are in a relationship permitting them to function in their intended manner. For instance, a promoter is operably linked to a coding sequence if the promoter affects its transcription or expression. A nucleic acid molecule is operatively linked or operably linked to, or operably associated with, an expression control sequence when the expression control sequence controls and regulates the transcription and translation of nucleic acid sequence. The term “operatively linked” includes having an appropriate start signal (e.g., ATG) in front of the nucleic acid sequence to be expressed and maintaining the correct reading frame to permit expression of the nucleic acid sequence under the control of the expression control sequence and production of the desired product encoded by the nucleic acid sequence. If a gene that one desires to insert into a recombinant DNA molecule does not contain an appropriate start signal, such a start signal can be inserted in front of the gene.

In accordance with the present invention there may be employed conventional molecular biology, microbiology, and recombinant DNA techniques within the skill of the art. Such techniques are explained fully in the literature. See, e.g., Sambrook et al, 2001, “Molecular Cloning: A Laboratory Manual”; Ausubel, ed., 1994, “Current Protocols in Molecular Biology” Volumes I-III; Celis, ed., 1994, “Cell Biology: A Laboratory Handbook” Volumes I-III; Coligan, ed., 1994, “Current Protocols in Immunology” Volumes I-III; Gait ed., 1984, “Oligonucleotide Synthesis”; Hames & Higgins eds., 1985, “Nucleic Acid Hybridization”; Hames & Higgins, eds., 1984, “Transcription And Translation”; Freshney, ed., 1986, “Animal Cell Culture”; IRL.

By an “effective amount” or a “sufficient amount” of an agent (e.g., a cargo), as used herein, is that amount sufficient to effect beneficial or desired results, such as clinical results, and, as such, an “effective amount” depends upon the context in which it is being applied. For example, in the context of administering an agent that employs a CRISPR component to genetically modify a gene, an effective amount of an agent is, for example, an amount sufficient to achieve increased or decreased expression of that gene, as compared to the response obtained without administration of the agent.

By “subject” is meant a human or non-human animal (e.g., a mammal).

By “treating” a disease, disorder, or condition in a subject is meant reducing at least one symptom of the disease, disorder, or condition by administrating a therapeutic agent to the subject. By “treating prophylactically” a disease, disorder, or condition in a subject is meant reducing the frequency of occurrence of or reducing the severity of a disease, disorder or condition by administering a therapeutic agent to the subject prior to the onset of disease symptoms. Beneficial or desired results can include, but are not limited to, alleviation or amelioration of one or more symptoms or conditions; diminishment of extent of disease, disorder, or condition; stabilized (i.e., not worsening) state of disease, disorder, or condition; preventing spread of disease, disorder, or condition; delay or slowing the progress of the disease, disorder, or condition; amelioration or palliation of the disease, disorder, or condition; and remission (whether partial or total), whether detectable or undetectable.

By “salt” is meant an ionic form of a compound or structure (e.g., any formulas, compounds, or compositions described herein), which includes a cation or anion compound to form an electrically neutral compound or structure. Salts are well known in the art. For example, non-toxic salts are described in Berge S M et al., “Pharmaceutical salts,” J. Pharm. Sci. 1977 January; 66(1):1-19; and in “Handbook of Pharmaceutical Salts: Properties, Selection, and Use,” Wiley-VCH, April 2011 (2nd rev. ed., eds. P. H. Stahl and C. G. Wermuth). The salts can be prepared in situ during the final isolation and purification of the compounds of the invention or separately by reacting the free base group with a suitable organic acid (thereby producing an anionic salt) or by reacting the acid group with a suitable metal or organic salt (thereby producing a cationic salt). Representative anionic salts include acetate, adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bicarbonate, bisulfate, bitartrate, borate, bromide, butyrate, camphorate, camphorsulfonate, chloride, citrate, cyclopentanepropionate, digluconate, dihydrochloride, diphosphate, dodecylsulfate, edetate, ethanesulfonate, fumarate, glucoheptonate, glucomate, glutamate, glycerophosphate, hemisulfate, heptonate, hexanoate, hydrobromide, hydrochloride, hydroiodide, hydroxyethanesulfonate, hydroxynaphthoate, iodide, lactate, lactobionate, laurate, lauryl sulfate, malate, maleate, malonate, mandelate, mesylate, methanesulfonate, methylbromide, methylnitrate, methylsulfate, mucate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, polygalacturonate, propionate, salicylate, stearate, subacetate, succinate, sulfate, tannate, tartrate, theophyllinate, thiocyanate, triethiodide, toluenesulfonate, undecanoate, valerate salts, and the like. Representative cationic salts include metal salts, such as alkali or alkaline earth salts, e.g., barium, calcium (e.g., calcium edetate), lithium, magnesium, potassium, sodium, and the like; other metal salts, such as aluminum, bismuth, iron, and zinc; as well as nontoxic ammonium, quaternary ammonium, and amine cations, including, but not limited to ammonium, tetramethylammonium, tetraethylammonium, methylamine, dimethylamine, trimethylamine, triethylamine, ethylamine, pyridinium, and the like. Other cationic salts include organic salts, such as chloroprocaine, choline, dibenzylethylenediamine, diethanolamine, ethylenediamine, methylglucamine, and procaine. Exemplary salts include pharmaceutically acceptable salts.

By “pharmaceutically acceptable salt” is meant a salt that is, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and animals without undue toxicity, irritation, allergic response and the like and are commensurate with a reasonable benefit/risk ratio.

By “pharmaceutically acceptable excipient” is meant any ingredient other than a compound or structure (e.g., any formulas, compounds, or compositions described herein) and having the properties of being nontoxic and non-inflammatory in a subject. Exemplary, non-limiting excipients include adjuvants, antiadherents, antioxidants, binders, carriers, coatings, compression aids, diluents, disintegrants, dispersing agents, dyes (colors), emollients, emulsifiers, fillers (diluents), film formers or coatings, flavors, fragrances, glidants (flow enhancers), isotonic carriers, lubricants, preservatives, printing inks, solvents, sorbents, stabilizers, suspensing or dispersing agents, surfactants, sweeteners, waters of hydration, or wetting agents. Any of the excipients can be selected from those approved, for example, by the United States Food and Drug Administration or other governmental agency as being acceptable for use in humans or domestic animals. Exemplary excipients include, but are not limited to alcohol, butylated hydroxytoluene (BHT), calcium carbonate, calcium phosphate (dibasic), calcium stearate, croscarmellose, cross-linked polyvinyl pyrrolidone, citric acid, crospovidone, cysteine, ethylcellulose, gelatin, glycerol, hydroxypropyl cellulose, hydroxypropyl methylcellulose, lactated Ringer's solution, lactose, magnesium stearate, maltitol, maltose, mannitol, methionine, methylcellulose, methyl paraben, microcrystalline cellulose, polyethylene glycol, polyol, polyvinyl pyrrolidone, povidone, pregelatinized starch, propyl paraben, retinyl palmitate, Ringer's solution, shellac, silicon dioxide, sodium carboxymethyl cellulose, sodium chloride injection, sodium citrate, sodium starch glycolate, sorbitol, starch (corn), stearic acid, stearic acid, sucrose, talc, titanium dioxide, vegetable oil, vitamin A, vitamin E, vitamin C, water, and xylitol.

As used herein, the terms “top,” “bottom,” “upper,” “lower,” “above,” and “below” are used to provide a relative relationship between structures. The use of these terms does not indicate or require that a particular structure must be located at a particular location in the apparatus.

By “alkenyl” is meant an optionally substituted C₂₋₂₄ alkyl group having one or more double bonds. The alkenyl group can be cyclic (e.g., C₃₋₂₄ cycloalkenyl) or acyclic. The alkenyl group can also be substituted or unsubstituted. For example, the alkenyl group can be substituted with one or more substitution groups, as described herein for alkyl.

By “alkyl” and the prefix “alk” is meant a branched or unbranched saturated hydrocarbon group of 1 to 24 carbon atoms, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, s-butyl, t-butyl, n-pentyl, isopentyl, s-pentyl, neopentyl, hexyl, heptyl, octyl, nonyl, decyl, dodecyl, tetradecyl, hexadecyl, eicosyl, tetracosyl, and the like. The alkyl group can be cyclic (e.g., C₃₋₂₄ cycloalkyl) or acyclic. The alkyl group can be branched or unbranched. The alkyl group can also be substituted or unsubstituted. For example, the alkyl group can be substituted with one, two, three or, in the case of alkyl groups of two carbons or more, four substituents independently selected from the group consisting of: (1) C₁₋₆ alkoxy (e.g., —OAk, in which Ak is an alkyl group, as defined herein); (2) C₁₋₆ alkylsulfinyl (e.g., —S(O)Ak, in which Ak is an alkyl group, as defined herein); (3) C₁₋₆ alkylsulfonyl (e.g., —SO₂Ak, in which Ak is an alkyl group, as defined herein); (4) amino (e.g., —NR^(N1)R^(N2), where each of R^(N1) and R^(N2) is, independently, H or optionally substituted alkyl, or R^(N1) and R^(N2), taken together with the nitrogen atom to which each are attached, form a heterocyclyl group); (5) aryl; (6) arylalkoxy (e.g., —OA^(L)Ar, in which A^(L) is an alkylene group and Ar is an aryl group, as defined herein); (7) aryloyl (e.g., —C(O)Ar, in which Ar is an aryl group, as defined herein); (8) azido (e.g., an —N3 group); (9) cyano (e.g., a —CN group); (10) carboxyaldehyde (e.g., a —C(O)H group); (11) C₃₋₈ cycloalkyl; (12) halo; (13) heterocyclyl (e.g., a 5-, 6- or 7-membered ring, unless otherwise specified, containing one, two, three, or four non-carbon heteroatoms (e.g., independently selected from the group consisting of nitrogen, oxygen, phosphorous, sulfur, or halo)); (14) heterocyclyloxy (e.g., —OHet, in which Het is a heterocyclyl group); (15) heterocyclyloyl (e.g., —C(O)Het, in which Het is a heterocyclyl group); (16) hydroxyl (e.g., a —OH group); (17)N-protected amino; (18) nitro (e.g., an —NO₂ group); (19) oxo (e.g., an ═O group); (20) C₃₋₈ spirocyclyl (e.g., an alkylene diradical, both ends of which are bonded to the same carbon atom of the parent group to form a spirocyclyl group); (21) C₁₋₆ thioalkoxy (e.g., —SAk, in which Ak is an alkyl group, as defined herein); (22) thiol (e.g., an —SH group); (23) —CO₂R^(A), where R^(A) is selected from the group consisting of (a) hydrogen, (b) C₁₋₆ alkyl, (c) C₄₋₁₈ aryl, and (d) C₁₋₆ alk-C₄₋₁₈ aryl; (24) —C(O)NR^(B)R^(C), where each of R^(B) and R^(C) is, independently, selected from the group consisting of (a) hydrogen, (b) C₁₋₆ alkyl, (c) C₄₋₁₈ aryl, and (d) C₁₋₆ alk-C₄₋₁₈ aryl; (25) —SO₂RD, where R^(D) is selected from the group consisting of (a) C₁₋₆ alkyl, (b) C₄₋₁₈ aryl, and (c) C₁₋₆ alk-C₄₋₁₈ aryl; (26) —SO₂NR^(E)R^(F), where each of R^(E) and R^(F) is, independently, selected from the group consisting of (a) hydrogen, (b) C₁₋₆ alkyl, (c) C₄₋₁₈ aryl, and (d) C₁₋₆ alk-C₄₋₁₈ aryl; and (27) —NR^(G)R^(H), where each of R^(G) and R^(H) is, independently, selected from the group consisting of (a) hydrogen, (b) an N-protecting group, (c) C₁₋₆ alkyl, (d) C₂₋₆ alkenyl, (e) C₂₋₆ alkynyl, (f) C₄₋₁₈ aryl, (g) C₁₋₆ alk-C₄₋₁₈ aryl, (h) C₃₋₈ cycloalkyl, and (i) C₁₋₆ alk-C₃₋₈ cycloalkyl, wherein in one embodiment no two groups are bound to the nitrogen atom through a carbonyl group or a sulfonyl group. The alkyl group can be a primary, secondary, or tertiary alkyl group substituted with one or more substituents (e.g., one or more halo or alkoxy). In some embodiments, the unsubstituted alkyl group is a C₁₋₃, C₁₋₆, C₁₋₁₂, C₁₋₁₆, C₁₋₁₈, C₁₋₂₀, or C₁₋₂₄ alkyl group.

By “alkylene” is meant a multivalent (e.g., bivalent, trivalent, tetravalent, etc.) form of an alkyl group, as described herein. Exemplary alkylene groups include methylene, ethylene, propylene, butylene, etc. In some embodiments, the alkylene group is a C₁₋₃, C₁₋₆, C₁₋₁₂, C₁₋₁₆, C₁₋₁₈, C₁₋₂₀, C₁₋₂₄, C₂₋₃, C₂₋₆, C₂₋₁₂, C₂₋₁₆, C₂₋₁₈, C₂₋₂₀, or C₂₋₂₄ alkylene group. The alkylene group can be branched or unbranched. The alkylene group can also be substituted or unsubstituted. For example, the alkylene group can be substituted with one or more substitution groups, as described herein for alkyl.

By “alkynyl” is meant an optionally substituted C₂₋₂₄ alkyl group having one or more triple bonds. The alkynyl group can be cyclic or acyclic and is exemplified by ethynyl, 1-propynyl, and the like. The alkynyl group can also be substituted or unsubstituted. For example, the alkynyl group can be substituted with one or more substitution groups, as described herein for alkyl.

By “amido” is meant —C(O)NR^(N1)R^(N2), where each of R^(N1) and R^(N2) is, independently, H, optionally substituted alkyl, or optionally substituted aryl; or where a combination of R^(N1) and R^(N2), taken together with the nitrogen atom to which each are attached, form a heterocyclyl group, as defined herein.

By “amino” is meant —NR^(N1)R^(N2), where each of R^(N1) and R^(N2) is, independently, H or optionally substituted alkyl, or R^(N1) and R^(N2), taken together with the nitrogen atom to which each are attached, form a heterocyclyl group, as defined herein.

By “aryl” is meant a group that contains any carbon-based aromatic group including, but not limited to, benzyl, naphthalene, phenyl, biphenyl, phenoxybenzene, and the like. The term “aryl” also includes “heteroaryl,” which is defined as a group that contains an aromatic group that has at least one heteroatom incorporated within the ring of the aromatic group. Examples of heteroatoms include, but are not limited to, nitrogen, oxygen, sulfur, and phosphorus. Likewise, the term “non-heteroaryl,” which is also included in the term “aryl,” defines a group that contains an aromatic group that does not contain a heteroatom. The aryl group can be substituted or unsubstituted. The aryl group can be substituted with one, two, three, four, or five substituents independently selected from the group consisting of: (1) C₁₋₆ alkanoyl (e.g., —C(O)Ak, in which Ak is an alkyl group, as defined herein); (2) C₁₋₆ alkyl; (3) C₁₋₆ alkoxy (e.g., —OAk, in which Ak is an alkyl group, as defined herein); (4) C₁₋₆ alkoxy-C₁₋₆ alkyl (e.g., an alkyl group, which is substituted with an alkoxy group —OAk, in which Ak is an alkyl group, as defined herein); (5) C₁₋₆ alkylsulfinyl (e.g., —S(O)Ak, in which Ak is an alkyl group, as defined herein); (6) C₁₋₆ alkylsulfinyl-C₁₋₆ alkyl (e.g., an alkyl group, which is substituted by an alkylsulfinyl group —S(O)Ak, in which Ak is an alkyl group, as defined herein); (7) C₁₋₆ alkylsulfonyl (e.g., —SO₂Ak, in which Ak is an alkyl group, as defined herein); (8) C₁₋₆ alkylsulfonyl-C₁₋₆ alkyl (e.g., an alkyl group, which is substituted by an alkylsulfonyl group —SO₂Ak, in which Ak is an alkyl group, as defined herein); (9) aryl; (10) amino (e.g., —NR^(N1)R^(N2) where each of R^(N1) and R^(N2) is, independently, H or optionally substituted alkyl, or R^(N) and R^(N2), taken together with the nitrogen atom to which each are attached, form a heterocyclyl group); (11) C₁₋₆ aminoalkyl (e.g., meant an alkyl group, as defined herein, substituted by an amino group); (12) heteroaryl; (13) C₁₋₆ alk-C₄₋₁₈ aryl (e.g., -A^(L)Ar, in which A^(L) is an alkylene group and Ar is an aryl group, as defined herein); (14) aryloyl (e.g., —C(O)Ar, in which Ar is an aryl group, as defined herein); (15) azido (e.g., an —N3 group); (16) cyano (e.g., a —CN group); (17) C₁₋₆ azidoalkyl (e.g., a —N₃ azido group attached to the parent molecular group through an alkyl group, as defined herein); (18) carboxyaldehyde (e.g., a —C(O)H group); (19) carboxyaldehyde-C₁₋₆ alkyl (e.g., -A^(L)C(O)H, in which A^(L) is an alkylene group, as defined herein); (20) C₃₋₈ cycloalkyl; (21) C₁₋₆ alk-C₃₋₈ cycloalkyl (e.g., -A^(L)Cy, in which A^(L) is an alkylene group and Cy is a cycloalkyl group, as defined herein); (22) halo (e.g., F, Cl, Br, or I); (23) C₁₋₆ haloalkyl (e.g., an alkyl group, as defined herein, substituted with one or more halo); (24) heterocyclyl; (25) heterocyclyloxy (e.g., —OHet, in which Het is a heterocyclyl group); (26) heterocyclyloyl (e.g., —C(O)Het, in which Het is a heterocyclyl group); (16) hydroxyl (e.g., a —OH group); (27) hydroxyl (e.g., a —OH group); (28) C₁₋₆ hydroxyalkyl (e.g., an alkyl group, as defined herein, substituted by one to three hydroxyl groups, with the proviso that no more than one hydroxyl group may be attached to a single carbon atom of the alkyl group); (29) nitro (e.g., an —NO₂ group); (30) C₁₋₆ nitroalkyl (e.g., an alkyl group, as defined herein, substituted by one to three nitro groups); (31)N-protected amino; (32)N-protected amino-C₁₋₆ alkyl; (33) oxo (e.g., an ═O group); (34) C₁₋₆ thioalkoxy (e.g., —SAk, in which Ak is an alkyl group, as defined herein); (35) thio-C₁₋₆ alkoxy-C₁₋₆ alkyl (e.g., an alkyl group, which is substituted by an thioalkoxy group —SAk, in which Ak is an alkyl group, as defined herein); (36) —(CH₂)_(r)CO₂R^(A), where r is an integer of from zero to four, and R^(A) is selected from the group consisting of (a) hydrogen, (b) C₁₋₆ alkyl, (c) C₄₋₁₈ aryl, and (d) C₁₋₆ alk-C₄₋₁₈ aryl; (37) —(CH₂)_(r)CONR^(B)R^(C), where r is an integer of from zero to four and where each R^(B) and R^(C) is independently selected from the group consisting of (a) hydrogen, (b) C₁₋₆ alkyl, (c) C₄₋₁₈ aryl, and (d) C₁₋₆ alk-C₄₋₁₈ aryl; (38) —(CH₂)_(r)SO₂R^(D), where r is an integer of from zero to four and where R^(D) is selected from the group consisting of (a) C₁₋₆ alkyl, (b) C₄₋₁₈ aryl, and (c) C₁₋₆ alk-C₄₋₁₈ aryl; (39) —(CH₂)_(r)SO₂NR^(E)R^(F), where r is an integer of from zero to four and where each of R^(E) and R^(F) is, independently, selected from the group consisting of (a) hydrogen, (b) C₁₋₆ alkyl, (c) C₄₋₁₈ aryl, and (d) C₁₋₆ alk-C₄₋₁₈ aryl; (40) —(CH₂)_(r)NR^(G)R^(H), where r is an integer of from zero to four and where each of R^(G) and R^(H) is, independently, selected from the group consisting of (a) hydrogen, (b) an N-protecting group, (c) C₁₋₆ alkyl, (d) C₂₋₆ alkenyl, (e) C₂₋₆ alkynyl, (f) C₄₋₁₈ aryl, (g) C₁₋₆ alk-C₄₋₁₈ aryl, (h) C₃₋₈ cycloalkyl, and (i) C₁₋₆ alk-C₃₋₈ cycloalkyl, wherein in one embodiment no two groups are bound to the nitrogen atom through a carbonyl group or a sulfonyl group; (41) thiol; (42) perfluoroalkyl (e.g., an alkyl group, as defined herein, having each hydrogen atom substituted with a fluorine atom); (43) perfluoroalkoxy (e.g., —ORf, in which Rf is an alkyl group, as defined herein, having each hydrogen atom substituted with a fluorine atom); (44) aryloxy (e.g., —OAr, where Ar is an optionally substituted aryl group, as described herein); (45) cycloalkoxy (e.g., —OCy, in which Cy is a cycloalkyl group, as defined herein); (46) cycloalkylalkoxy (e.g., —OA^(L)Cy, in which A^(L) is an alkylene group and Cy is a cycloalkyl group, as defined herein); and (47) arylalkoxy (e.g., —OA^(L)Ar, in which A^(L) is an alkylene group and Ar is an aryl group, as defined herein). In particular embodiments, an unsubstituted aryl group is a C₄₋₁₈, C₄₋₁₄, C₄₋₁₂, C₄₋₁₀, C₆₋₁₈, C₆₋₁₄, C₆₋₁₂, or C₆₋₁₀ aryl group.

By “arylene” is meant a multivalent (e.g., bivalent, trivalent, tetravalent, etc.) form of an aryl group, as described herein. Exemplary arylene groups include phenylene, naphthylene, biphenylene, triphenylene, diphenyl ether, acenaphthenylene, anthrylene, or phenanthrylene. In some embodiments, the arylene group is a C₄₋₁₈, C₄₋₁₄, C₄₋₁₂, C₄₋₁₀, C₆₋₁₈, C₆₋₁₄, C₆₋₁₂, or C₆₋₁₀ arylene group. The arylene group can be branched or unbranched. The arylene group can also be substituted or unsubstituted. For example, the arylene group can be substituted with one or more substitution groups, as described herein for aryl.

By “azido” is meant an —N₃ group.

By “carbamido” is meant —NR^(N1)C(O)NR^(N2)R^(N3), where each of R^(N1) and R^(N2) and R^(N3) is, independently, H, optionally substituted alkyl, or optionally substituted aryl; or where a combination of R^(N2) and R^(N3), taken together with the nitrogen atom to which each are attached, form a heterocyclyl group, as defined herein.

By “carbonyl” is meant a —C(O)— group, which can also be represented as >C═O.

By “carboxyl” is meant a —CO₂H group.

By “halo” is meant F, Cl, Br, or I.

By “heteroalkyl” is meant an alkyl group, as defined herein, containing one, two, three, or four non-carbon heteroatoms (e.g., independently selected from the group consisting of nitrogen, oxygen, phosphorous, sulfur, or halo).

By “heteroalkylene” is meant a divalent form of an alkylene group, as defined herein, containing one, two, three, or four non-carbon heteroatoms (e.g., independently selected from the group consisting of nitrogen, oxygen, phosphorous, sulfur, or halo).

By “heteroaryl” is meant a subset of heterocyclyl groups, as defined herein, which are aromatic, i.e., they contain 4n+2 pi electrons within the mono- or multicyclic ring system.

By “heterocyclyl” is meant a 5-, 6- or 7-membered ring, unless otherwise specified, containing one, two, three, or four non-carbon heteroatoms (e.g., independently selected from the group consisting of nitrogen, oxygen, phosphorous, sulfur, or halo). The 5-membered ring has zero to two double bonds and the 6- and 7-membered rings have zero to three double bonds. The term “heterocyclyl” also includes bicyclic, tricyclic and tetracyclic groups in which any of the above heterocyclic rings is fused to one, two, or three rings independently selected from the group consisting of an aryl ring, a cyclohexane ring, a cyclohexene ring, a cyclopentane ring, a cyclopentene ring, and another monocyclic heterocyclic ring, such as indolyl, quinolyl, isoquinolyl, tetrahydroquinolyl, benzofuryl, benzothienyl and the like. Heterocyclics include thiiranyl, thietanyl, tetrahydrothienyl, thianyl, thiepanyl, aziridinyl, azetidinyl, pyrrolidinyl, piperidinyl, azepanyl, pyrrolyl, pyrrolinyl, pyrazolyl, pyrazolinyl, pyrazolidinyl, imidazolyl, imidazolinyl, imidazolidinyl, pyridyl, homopiperidinyl, pyrazinyl, piperazinyl, pyrimidinyl, pyridazinyl, oxazolyl, oxazolidinyl, isoxazolyl, isoxazolidiniyl, morpholinyl, thiomorpholinyl, thiazolyl, thiazolidinyl, isothiazolyl, isothiazolidinyl, indolyl, quinolinyl, isoquinolinyl, benzimidazolyl, benzothiazolyl, benzoxazolyl, furyl, thienyl, thiazolidinyl, isothiazolyl, isoindazoyl, triazolyl, tetrazolyl, oxadiazolyl, uricyl, thiadiazolyl, pyrimidyl, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothienyl, dihydrothienyl, dihydroindolyl, tetrahydroquinolyl, tetrahydroisoquinolyl, pyranyl, dihydropyranyl, dithiazolyl, benzofuranyl, benzothienyl, and the like.

By “hydroxyl” is meant —OH.

By “imido” is meant —C(O)NR^(N1)C(O)—, where R^(N1) is, independently, H, optionally substituted alkyl, or optionally substituted aryl.

By “protecting group” is meant any group intended to protect a reactive group against undesirable synthetic reactions. Commonly used protecting groups are disclosed in “Greene's Protective Groups in Organic Synthesis,” John Wiley & Sons, New York, 2007 (4th ed., eds. P. G. M. Wuts and T. W. Greene), which is incorporated herein by reference. O-protecting groups include an optionally substituted alkyl group (e.g., forming an ether with reactive group O), such as methyl, methoxymethyl, methylthiomethyl, benzoyloxymethyl, t-butoxymethyl, etc.; an optionally substituted alkanoyl group (e.g., forming an ester with the reactive group O), such as formyl, acetyl, chloroacetyl, fluoroacetyl (e.g., perfluoroacetyl), methoxyacetyl, pivaloyl, t-butylacetyl, phenoxyacetyl, etc.; an optionally substituted aryloyl group (e.g., forming an ester with the reactive group O), such as —C(O)—Ar, including benzoyl; an optionally substituted alkylsulfonyl group (e.g., forming an alkylsulfonate with reactive group O), such as —SO₂—R^(S1), where R^(S1) is optionally substituted C₁₋₁₂ alkyl, such as mesyl or benzylsulfonyl; an optionally substituted arylsulfonyl group (e.g., forming an arylsulfonate with reactive group O), such as —SO₂—R^(S4), where R^(S4) is optionally substituted C₄₋₁₈ aryl, such as tosyl or phenylsulfonyl; an optionally substituted alkoxycarbonyl or aryloxycarbonyl group (e.g., forming a carbonate with reactive group O), such as —C(O)—OR^(T1), where R^(T1) is optionally substituted C₁₋₁₂ alkyl or optionally substituted C₄₋₁₈ aryl, such as methoxycarbonyl, methoxymethylcarbonyl, t-butyloxycarbonyl (Boc), or benzyloxycarbonyl (Cbz); or an optionally substituted silyl group (e.g., forming a silyl ether with reactive group O), such as —Si—(R^(T2))₃, where each R^(T2) is, independently, optionally substituted C₁₋₁₂ alkyl or optionally substituted C₄₋₁₈ aryl, such as trimethylsilyl, t-butyldimethylsilyl, or t-butyldiphenylsilyl. N-protecting groups include, e.g., formyl, acetyl, benzoyl, pivaloyl, t-butylacetyl, alanyl, phenylsulfonyl, benzyl, Boc, and Cbz. Such protecting groups can employ any useful agent to cleave the protecting group, thereby restoring the reactivity of the unprotected reactive group.

By “thio” is meant an —S— group.

By “thiol” is meant an —SH group.

By “attaching,” “attachment,” or related word forms is meant any covalent or non-covalent bonding interaction between two components. Non-covalent bonding interactions include, without limitation, hydrogen bonding, ionic interactions, halogen bonding, electrostatic interactions, 7 bond interactions, hydrophobic interactions, inclusion complexes, clathration, van der Waals interactions, and combinations thereof.

Other features and advantages of the invention will be apparent from the following description and the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A-1C shows exemplary constructs. Provided are (A) an exemplary method 100 for providing a non-limiting construct having a core 101, a spacer 103, a cargo 104, and an outer layer 105; (B) another exemplary construct 1000; and (C) yet another exemplary construct 1500.

FIG. 2A-2D shows exemplary cores formed by (A, B) an aerosol-based process (evaporation-induced self-assembly, EISA) and (C, D) a solution-based process. Provided are micrographs of cores (A,C) before pore expansion and (B,D) after pore expansion with a swelling agent.

FIG. 3A-3B shows release studies of GFP-bound silica beads, in which GFP (an exemplary cargo) was bound to silica by way of (A) a spacer having a cleavable disulfide bond. Provided are (B) resultant fluorescence intensity with bound GFP in the absence of glutathione (GSH) and released GFP in the presence of 5 mM GSH.

FIG. 4A-4D shows characterization of GFP-bound expanded pore mesoporous silica nanoparticle (EP-MSNP), in which His-tagged GFP was attached to EP-MSNPs having a nickel(II)-nitrilotriacetic acid (Ni-NTA)-based spacer. Provided are data for particles (A,C) without a lipid layer and (B,D) with a lipid layer.

FIG. 5 shows the effect of cargo and the composition of the outer layer on particle size (Rh, nm). Provided are size data for (A) EP-MSNPs; (B) EP-MSNPs with a Ni-NTA-based spacer; (C) EP-MSNPs having a spacer and a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid layer; (D) EP-MSNPs having a spacer, attached GFP cargo, and a POPC lipid layer; (E) EP-MSNPs having a spacer, attached GFP cargo, and a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipid layer; (F) EP-MSNPs having a spacer and a Cas9 cargo; and (G) EP-MSNPS having a spacer and a RNP cargo.

FIG. 6A-6B shows characteristics of an exemplary CRISPR component. Provided are images of gels showing (A) production and purification of a Cas9 protein and (B) a digestion assay conducted with Cas9/guide RNA.

FIG. 7A-7B shows Cas9 release and activity from aerosol-generated EP-MSNPs. Provided are gels showing cleavage products for assays conducted with (A) NLS-Cas9 that was buffer-exchanged and bound to particles and (B) NLS-Cas9 either before or after buffer exchange in an in vitro assay, as control.

FIG. 8A-8C shows exemplary methods for providing a construct and its use for in vitro gene editing. Provided are schematics of (A) an exemplary method for loading RNP within a construct and (B) an exemplary method for in vitro gene editing by use of an RNP-loaded construct. Also provided are (C) fluorescence photomicrographs showing delivery of an RNP-loaded construct to a reporter cell line with an AAVS1 target site, in which effective gene-editing by the RNP results in a frameshift mutation and GFP expression.

FIG. 9A-9C shows delivery of lipid-coated mesoporous silica nanoparticles and Cas9 into mammalian cells via a reducible di-sulfide spacer. Provided are (A) mesoporous silica nanoparticle (MSNP) cores that were functionalized with a PEG-Ni-NTA disulfide spacer in order to attach a 6XHis-tagged Cas9 protein complexed with guide RNA. Also provided are (B) results from controlled release of a cargo (e.g., Cas9) by incubating with a cleaving agent, in which LC-MSN-PEG-SS-PEG-Ni-NTA-RNP were incubated with (+) and without (−) a cleaving agent (e.g., a reducing agent, such as DTT). The supernatant fraction and pellet fraction (pelleted NP fraction via centrifugation) were analyzed using gel electrophoresis and indicated Cas9/gRNA RNPs were released only under reducing conditions. (C) When lipid-coated reducible RNP complexed NPs were incubated with mammalian cell cultures (A549 cells) for 24 hours, the labeled Cas9 (green) was internalized but not co-localized with endosomes.

FIG. 10A-10E shows exemplary linking agents. Provided are schematics of (A) an exemplary method employing linking agent L1 to provide a construct having a nanoparticle (NP) core, a spacer, and an attached cargo, (B) another exemplary spacer having a reactive group L″ that interacts with a reactive group R¹ present on a cargo, and (C) yet other exemplary spacers present between the NP and the cargo. Also provided are (D) another exemplary spacer and (B) another exemplary method employing linking agent L2 to provide a construct having a NP core, a spacer, and an attached cargo.

FIG. 11A-11C shows further exemplary linking agents and spacers. Provided are schematics of (A) exemplary spacers (i)-(iii) present between a core and a cargo, (B) an exemplary reaction scheme between a linking agent and a reactive group present on a cargo, thereby forming a spacer between the core and the cargo, and (C) yet another reaction scheme between another linking agent and a reactive group present on a cargo.

FIG. 12 shows an exemplary CRISPR component includes a guiding component 90 to bind to the target sequence 97, as well as a nuclease 98 (e.g., a Cas nuclease or an endonuclease, such as a Cas endonuclease) that interacts with the guiding component and the target sequence.

FIG. 13A-13C shows non-limiting CRISPR components. Provided are schematics of (A) a non-limiting guiding component 300 having a targeting portion 304, a first portion 301, a second portion 302, and a linker 303 disposed between the first and second portions; (B) another non-limiting guiding component 350 having a targeting portion 354, a first portion 351, a second portion 352 having a hairpin, and a linker 353 disposed between the first and second portions; and (C) non-limiting interactions between the guiding component 400, the genomic sequence 412, and the first and second portion 401,402. As can be seen, the target sequence 411 of the genomic sequence 412 is targeted by way of non-covalent binding 421 to the targeting portion 404, and secondary structure can be optionally implemented by way of non-covalent binding 422 between the first portion 401 and the second portion 402. The targeting portion 404, first portion 401, linker 403, and second portion 402 can be attached in any useful manner (e.g., to provide a 5′ end 405 and a 3′ end 406).

FIG. 14A-14H shows non-limiting amino acid sequences for various nucleases. Provided are sequences for (A) a Cas9 endonuclease for S. pyogenes serotype M1 (SEQ ID NO:110), (B) a deactivated Cas9 having D10A and H840A mutations (SEQ ID NO:111), (C) a Cas protein Csn1 for S. pyogenes (SEQ ID NO:112), (D) a Cas9 endonuclease for F. novicida U112 (SEQ ID NO:113), (E) a Cas9 endonuclease for S. thermophilus 1 (SEQ ID NO:114), (F) a Cas9 endonuclease for S. thermophilus 2 (SEQ ID NO:115), (G) a Cas9 endonuclease for L. innocua (SEQ ID NO:116), and (H) a Cas9 endonuclease for W. succinogenes (SEQ ID NO:117).

FIG. 15 shows non-limiting nucleic acid sequences of crRNA that can be employed as a first portion in any guiding component described herein. Provided are sequences for S. pyogenes (SEQ ID NO:20), L. innocua (SEQ ID NO:21), S. thermophilus 1 (SEQ ID NO:22), S. thermophilus 2 (SEQ ID NO:23), F. novicida (SEQ ID NO:24), and W. succinogenes (SEQ ID NO:25). Also provided are various consensus sequences (SEQ ID NOs:26-32), in which each X, independently, can be absent, A, C, T, G, or U, as well as modified forms thereof (e.g., as described herein). In another embodiment, for each consensus sequence (SEQ ID NOs:26-32), each X at each position is a nucleic acid (or a modified form thereof) that is provided in an aligned reference sequence. For instance, for consensus SEQ ID NO:26, the first position includes an X, and this X can be absent or any nucleic acid (e.g., A, C, T, G, or U, as well as modified forms thereof). Alternatively, this X can be any nucleic acid provided in an aligned reference sequence (e.g., aligned reference sequences SEQ ID NO:20-25 for the consensus sequence in SEQ ID NO:26). Thus, X at position 1 in SEQ ID NO:26 can also be G (as in SEQ ID NOs:20-23 and 25) or C (as in SEQ ID NO:24), in which this subset of substitutions is defined as a conservative subset. Similarly, for each X at each position for the consensus sequences (SEQ ID NOs:26-32), conservative subsets can be determined based on FIG. 15, and these consensus sequences include nucleic acid sequences encompassed by such conservative subsets. Gray highlight indicates a conserved nucleic acid, and the dash indicates an absent nucleic acid.

FIG. 16A-16C shows non-limiting nucleic acid sequences of tracrRNA that can be employed as a second portion and/or linker in any guiding component described herein. Provided are sequences for S. pyogenes (SEQ ID NO:40), L. innocua (SEQ ID NO:41), S. thermophilus 1 (SEQ ID NO:42), S. thermophilus 2 (SEQ ID NO:43), F. novicida 1 (SEQ ID NO:44), F. novicida 2 (SEQ ID NO:45), W. succinogenes 1 (SEQ ID NO:46), and W. succinogenes 2 (SEQ ID NO:47). Also provided are various consensus sequences (SEQ ID NOs:48-54), in which each Z, independently, can be absent, A, C, T, G, or U, as well as modified forms thereof (e.g., as described herein). Consensus sequences are shown for (A) an alignment of all SEQ ID NOs:40-47, providing consensus sequences SEQ ID NOs:48-50; (B) an alignment of SEQ ID NOs:40-43, providing consensus sequences SEQ ID NOs:51-52; and (C) an alignment of SEQ ID NOs:44-47, providing consensus sequences SEQ ID NOs:53-54. In another embodiment, for each consensus sequence (SEQ ID NOs:48-54), each Z at each position is a nucleic acid (or a modified form thereof) that is provided in an aligned reference sequence. For instance, for consensus SEQ ID NO:48, the first position includes a Z, and this Z can be absent or any nucleic acid (e.g., A, C, T, G, or U, as well as modified forms thereof). Alternatively, this Z can be any nucleic acid provided in an aligned reference sequence (e.g., aligned reference sequences SEQ ID NO:40-47 for the consensus sequence in SEQ ID NO:48). Thus, Z at position 2 in SEQ ID NO:48 can also be U (as in SEQ ID NOs:40, 41, and 43-47) or G (as in SEQ ID NO:42), in which this subset of substitutions is defined as a conservative subset. Similarly, for each Z at each position for the consensus sequences (SEQ ID NOs:48-54), conservative subsets can be determined based on FIG. 16A-16C, and these consensus sequences include nucleic acid sequences encompassed by such conservative subsets. Gray highlight indicates a conserved nucleic acid, and the dash indicates an absent nucleic acid.

FIG. 17 shows non-limiting nucleic acid sequences of extended tracrRNA that can be employed as a second portion and/or linker in any guiding component described herein. Provided are sequences for S. pyogenes (SEQ ID NO:60), L. innocua (SEQ ID NO:61), S. thermophilus 1 (SEQ ID NO:62), and S. thermophilus 2 (SEQ ID NO:63). Also provided are various consensus sequences (SEQ ID NOs:64-65), in which each Z, independently, can be absent, A, C, T, G, or U, as well as modified forms thereof (e.g., as described herein). In another embodiment, for each consensus sequence (SEQ ID NOs:64-65), each Z at each position is a nucleic acid (or a modified form thereof) that is provided in an aligned reference sequence. For instance, for consensus SEQ ID NO:64, the first position includes a Z, and this Z can be absent or any nucleic acid (e.g., A, C, T, G, or U, as well as modified forms thereof). Alternatively, this Z can be any nucleic acid provided in an aligned reference sequence (e.g., aligned reference sequences SEQ ID NO:60-63 for the consensus sequence in SEQ ID NO:64). Thus, Z at position 1 in SEQ ID NO:64 can also be absent (as in SEQ ID NO:60), A (as in SEQ ID NO:61), or U (as in SEQ ID NOs:63-64), in which this subset of substitutions is defined as a conservative subset. Similarly, for each Z at each position for the consensus sequences (SEQ ID NOs:64-65), conservative subsets can be determined based on FIG. 17, and these consensus sequences include nucleic acid sequences encompassed by such conservative subsets. Gray highlight indicates a conserved nucleic acid, and the dash indicates an absent nucleic acid.

FIG. 18 shows non-limiting nucleic acid sequences of a guiding component (e.g., a synthetic, non-naturally occurring guiding component) having a generic structure of A-L-B, in which A includes a first portion (e.g., any one of SEQ ID NOs:20-32, or a fragment thereof), L is a linker (e.g., a covalent bond, a nucleic acid sequence, a fragment of any one of SEQ ID NOs:40-54 and 60-65, or any other useful linker), and B is a second portion (e.g., any one of SEQ ID NOs:40-54 and 60-65, or a fragment thereof). Also provided are various embodiments of single-stranded guiding components (SEQ ID NOs:80-93). Exemplary non-limiting guiding components include SEQ ID NO:81, or a fragment thereof, where X at each position is defined as in SEQ ID NO:26 and Z at each position is as defined in SEQ ID NO:48; SEQ ID NO:82, or a fragment thereof, where X at each position is defined as in SEQ ID NO:27 and Z at each position is as defined in SEQ ID NO:49; SEQ ID NO:83, where X at each position is defined as in SEQ ID NO:28 and Z at each position is as defined in SEQ ID NO:49; SEQ ID NO:84, or a fragment thereof, where X at each position is defined as in SEQ ID NO:27 and Z at each position is as defined in SEQ ID NO:65; SEQ ID NO:85, or a fragment thereof, where X at each position is defined as in SEQ ID NO:28 and Z at each position is as defined in SEQ ID NO:65; SEQ ID NO:86, or a fragment thereof, where X at each position is defined as in SEQ ID NO:29 and Z at each position is defined as in SEQ ID NO:51; SEQ ID NO:87, or a fragment thereof, where X at each position is defined as in SEQ ID NO:30 and Z at each position is defined as in SEQ ID NO:51; SEQ ID NO:88, or a fragment thereof, where X at each position is defined as in SEQ ID NO:30 and Z at each position is defined as in SEQ ID NO:52; SEQ ID NO:89, or a fragment thereof, where X at each position is defined as in SEQ ID NO:30 and Z at each position is defined as in SEQ ID NO:65; SEQ ID NO:90, or a fragment thereof, where X at each position is defined as in SEQ ID NO:31 and Z at each position is defined as in SEQ ID NO:51; SEQ ID NO:91, or a fragment thereof, where X at each position is defined as in SEQ ID NO:32 and Z at each position is as defined in SEQ ID NO:53; SEQ ID NO:92, or a fragment thereof, where X at each position is defined as in SEQ ID NO:32 and Z at each position is as defined in SEQ ID NO:54; and SEQ ID NO:93, or a fragment thereof, where X at each position is defined as in SEQ ID NO:32 and Z at each position is defined as in SEQ ID NO:65. The fragment can include any useful number of nucleotides (e.g., any number of contiguous nucleotides, such as a fragment including about 4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 18, 20, or more contiguous nucleotides of any sequences described herein, such as a sequence for the first portion, e.g., any one of SEQ ID NOs:20-32; and also such as a fragment including about 4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 18, 20, 24, 26, 28, 30, 32, 34, 38, 36, 40, or more contiguous nucleotides of any sequences described herein, such as a sequence for the first portion, e.g., any one of SEQ ID NOs:40-54 and 60-65).

FIG. 19 shows additional non-limiting nucleic acid sequences of a guiding component (e.g., a synthetic, non-naturally occurring guiding component). Provided are various embodiments of single-stranded guiding components (SEQ ID NOs:100-103). Exemplary non-limiting guiding components include SEQ ID NO:100, or a fragment thereof, where n at each of positions 1-80 can be present or absent such that this region can contain anywhere from 12 to 80 nucleotides and n is A, C, T, G, U, or modified forms thereof; and where n at each of positions 93-192 can be present or absent such that this region can contain anywhere from 3 to 100 nucleotides and n is A, C, T, G, U, or modified forms thereof; SEQ ID NO:101, or a fragment thereof, where n at each of positions 1-80 can be present or absent such that this region can contain anywhere from 12 to 80 nucleotides and n is A, C, T, G, U, or modified forms thereof; and where n at each of positions 93-192 can be present or absent such that this region can contain anywhere from 3 to 100 nucleotides and n is A, C, T, G, U, or modified forms thereof; SEQ ID NO:102, or a fragment thereof, where n at each of positions 1-80 can be present or absent such that this region can contain anywhere from 12 to 80 nucleotides and n is A, C, T, G, U, or modified forms thereof; and SEQ ID NO:103, or a fragment thereof, where n at each of positions 1-80 can be present or absent such that this region can contain anywhere from 12 to 80 nucleotides and n is A, C, T, G, U, or modified forms thereof.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates, in part, to particle-based constructs configured to transport a cargo in vitro and in vivo. In particular embodiments, the construct includes a porous nanoparticle core, in which the pores are employed to completely or partially confine the cargo. In some non-limiting instances, the size of the cargo and the core are both in the nanoscale regime, such that a pore size necessary to confine the cargo approaches the dimension of the nanoparticle core. Thus, a spacer can be useful to colocalize the cargo in proximity to the pore, even if the pore's size does not fully accommodate the entirety of the cargo.

The construct can include any useful component and can be assembled in any useful process. FIG. 1A provides an exemplary method 100 for assembling a construct. As can be seen, the method can include providing a core 101 including a plurality of pores 102. The pores can be in fluidic communication with the external surface. Furthermore, a first pore can optionally be in fluidic communication with a second pore. The pores can be characterized in any useful manner, such as, e.g., by an average dimension of the plurality of pores.

Optionally, the method can include expanding the pores present in the core. In this instance, the pores of the initial core can be characterized by a first dimension. After expansion, the initial core can include a plurality of expanded pores, where an average dimension of the plurality of expanded pores is characterized by a second dimension that is greater than the first dimension. Pore expansion can be accomplished in any useful manner, e.g., by use of a swelling agent to expand an initial pore size to a larger pore size.

Spacers can be used to attach a cargo to the core. As seen in FIG. 1A, the method can optionally include installing 110 a spacer 103 to be disposed within at least one pore and/or upon the external surface of the core. The spacer can be installed by use of a linking agent (e.g., L¹-R^(L)-L², in which R^(L) is a linking group such as any described herein; each of L¹ and L² is, independently, a reactive group such as any functional group described herein; and each of L¹ and L² can be the same or different). The linking agent can include a first reactive group to form a bond with the core, as well as a second reactive group to form a bond with the cargo. In some instance, the linking agent be divalent (having two reactive groups) or multivalent (having more than two reactive groups).

The cargo can be introduced to the core in any useful manner, thereby providing a loaded core. As seen in FIG. 1A, the method can include binding 120 a cargo 104 to a spacer. In one non-limiting instance, the installed spacer 103 can include a reactive group that interacts with a reactive group present on the cargo, thereby forming a bond (e.g., a covalent or non-covalent bond).

Then, an outer layer can be provided on the external surface of the core. The outer layer can have any useful composition, e.g., a lipid, a polymer, or both. In one instance, the method includes providing 130 an outer layer 130, thereby forming an exemplary construct. The outer layer can be formed in any useful manner, e.g., by exposing the loaded core to a lipid formulation to form an outer lipid layer.

The outer layer can include one or more moieties (e.g., targeting ligands, PEG, etc.). These moieties can be introduced before or after providing the outer layer. In yet other embodiments, the moieties can be introduced simultaneously with providing the outer layer. In the case for forming an outer lipid layer, a lipid formulation including desired lipids, components (e.g., cholesterol), and moieties (e.g., targeting ligands) can be prepared; and the resulting lipid formulation can be used to form the outer layer. As seen in FIG. 1A, the method can optionally include providing 140 one or moieties 106, thereby forming another exemplary construct.

Any useful construct can be employed. As seen in FIG. 1A, one exemplary construct includes a core 101 having a plurality of pores 102, a spacer 102 disposed within a pore, a cargo 104 attached to the spacer, and an outer layer 105 optionally including a moiety 106. Other constructs can be implemented. For instance, FIG. 1B provides another exemplary construct 1000 having interconnected pores 1002 within the core 1001, spacers 1003 disposed on an external surface of the core, a cargo 1004 attached to the spacer, and an outer layer 1005. In another instance, FIG. 1C provides yet another exemplary construct 1500 having interconnected pores 1502 within the core 1501, spacers 1503 disposed on an external surface of the core or within a pore, a cargo 1504 attached to the spacer, and an outer layer 1505. Other types of constructs, cores, cargos, spacers, and outer layers are described herein.

Core

The present invention relates, in part, to a particle having a core. The core can provide any useful benefit. In particular, non-limiting embodiments, the core provides a surface upon which an outer layer can be supported. In other non-limiting embodiments, the core provides a charged surface that allows for electrostatic interactions with the cargo and/or the outer layer, or a portion thereof.

The core can be characterized in any useful manner. In one instance, the core can be characterized by a first dimension (e.g., core circumference, pore size of the core, core diameter, core length, or core width). Exemplary values for a core dimension (e.g., core circumference, core diameter, core length, or core width, as well as an average or mean value for any of these) include, without limitation, greater than about 1 nm (e.g., greater than about 5 nm, 10 nm, 20 nm, 30 nm, 40 nm, 50 nm, 60 nm, 70 nm, 80 nm, 90 nm, 100 nm, 125 nm, 150 nm, 200 nm, 300 nm, 500 nm, 750 nm, 1 m, 2 m, 5 m, 10 m, 20 m, or more), including of from about 5 nm to about 300 nm (e.g., from 5 nm to 20 nm, 5 nm to 30 nm, 5 nm to 40 nm, 5 nm to 50 nm, 5 nm to 75 nm, 5 nm to 100 nm, 5 nm to 150 nm, 5 nm to 200 nm, 5 nm to 250 nm, 10 nm to 20 nm, 10 nm to 30 nm, 10 nm to 40 nm, 10 nm to 50 nm, 10 nm to 75 nm, 10 nm to 100 nm, 10 nm to 150 nm, 10 nm to 200 nm, 10 nm to 250 nm, 10 nm to 300 nm, 25 nm to 30 nm, 25 nm to 40 nm, 25 nm to 50 nm, 25 nm to 75 nm, 25 nm to 100 nm, 25 nm to 150 nm, 25 nm to 200 nm, 25 nm to 250 nm, 25 nm to 300 nm, 50 nm to 75 nm, 50 nm to 100 nm, 50 nm to 150 nm, 50 nm to 200 nm, 50 nm to 250 nm, 50 nm to 300 nm, 75 nm to 100 nm, 75 nm to 150 nm, 75 nm to 200 nm, 75 nm to 250 nm, 75 nm to 300 nm, 100 nm to 150 nm, 100 nm to 200 nm, 100 nm to 250 nm, 100 nm to 300 nm, 150 nm to 200 nm, 150 nm to 250 nm, 150 nm to 300 nm, 200 nm to 250 nm, 200 nm to 300 nm, 250 nm to 300 nm, or 275 nm to 300 nm). In one instance, the particle includes a porous core (e.g., a silica core that is spherical and ranges in diameter from about 10 nm to about 250 nm (e.g., having a mean diameter of about 150 nm)). In particular embodiments, the silica core is monodisperse or polydisperse in size distribution.

The core can be further characterized by an electrostatic property. In some embodiments, the core has a negative charge (e.g., a net negative charge), such as a zeta potential of from about −10 mV to about −200 mV (e.g., from −10 mV to −100 mV, −10 mV to −75 mV, −10 mV to −50 mV, −10 mV to −30 mV, −15 mV to −100 mV, −15 mV to −75 mV, −15 mV to −50 mV, −15 mV to −30 mV, −20 mV to −100 mV, −20 mV to −75 mV, −20 mV to −50 mV, −20 mV to −30 mV, −30 mV to −100 mV, −30 mV to −75 mV, −30 mV to −50 mV, −40 mV to −100 mV, −40 mV to −75 mV, −40 mV to −50 mV, −50 mV to −100 mV, −50 mV to −75 mV, −60 mV to −100 mV, or −60 mV to −75 mV).

The core can be porous. In particular embodiments, the pore has a dimension (e.g., average pore size, pore diameter, pore radius, pore circumference, pore length, pore width, or pore depth) that is greater than about 0.5 nm (e.g., of from about 0.5 nm to about 30 nm, including from 0.5 nm to 10 nm, 0.5 nm to 20 nm, 0.5 nm to 25 nm, 1 nm to 10 nm, 1 nm to 15 nm, 1 nm to 20 nm, 1 nm to 25 nm, 1 nm to 30 nm, 2 nm to 5 nm, 2 nm to 10 nm, 2 nm to 20 nm, 2 nm to 25 nm, or 2 nm to 30 nm).

A particle or a portion thereof (e.g., a core) may have a variety of shapes and cross-sectional geometries that may depend, in part, upon the process used to produce the particles. The core or particle can be a nanoparticle (e.g., having a diameter less than about 1 m) or a microparticle (e.g., having a diameter greater than or equal to about 1 m). In one embodiment, a core or particle may have a shape that is a sphere, a donut (toroidal), a rod, a tube, a flake, a fiber, a plate, a wire, a cube, or a whisker. A collection of cores may have two or more of the aforementioned shapes. In one embodiment, a cross-sectional geometry of the core may be one or more of circular, ellipsoidal, triangular, rectangular, or polygonal. In one embodiment, a core may consist essentially of non-spherical cores. For example, such cores may have the form of ellipsoids, which may have all three principal axes of differing lengths, or may be oblate or prelate ellipsoids of revolution. Non-spherical cores alternatively may be laminar in form, wherein laminar refers to particles in which the maximum dimension along one axis is substantially less than the maximum dimension along each of the other two axes. Non-spherical cores may also have the shape of frusta of pyramids or cones, or of elongated rods. In one embodiment, the cores may be irregular in shape. In one embodiment, a plurality of cores may consist essentially of spherical cores. Particles and cores for use in the present invention may be PEGylated and/or aminated as otherwise described in Int. Pub. Nos. WO 2015/042268 and WO 2015/042279, which is incorporated herein by reference in their entirety.

The particle size distribution (e.g., size of the core for the protocell or a size of the silica carrier), according to the present invention, depends on the application, but is principally monodisperse (e.g., a uniform sized population varying no more than about 5-20% in diameter, as otherwise described herein). In certain embodiments, particles or cores can range, e.g., from around 1 nm to around 500 nm in size, including all integers and ranges there between. The size is measured as the longest axis of the core. In various embodiments, the cores are from around 5 nm to around 500 nm and from around 10 nm to around 100 nm in size. In certain alternative embodiments, the cores or particles are monodisperse and range in size from about 25 nm to about 300 nm. The sizes used preferably include 50 nm (+/−10 nm) and 150 nm (+/−15 nm), within a narrow monodisperse range, but may be more narrow in range.

When the core is porous, the pores can be from around 0.5 nm to about 25 nm in diameter, often about 1 to around 20 nm in diameter, including all integers and ranges there between. In one embodiment, the pores are from around 1 to around 10 nm in diameter. In one embodiment, around 90% of the pores are from around 1 to around 20 nm in diameter. In another embodiment, around 95% of the pores are around 1 to around 20 nm in diameter.

In certain embodiments, preferred cores or particles according to the present invention: are monodisperse and range in size from about 25 nm to about 300 nm; exhibit stability (colloidal stability); have single cell binding specification to the substantial exclusion of non-targeted cells; are anionic, neutral or cationic for specific targeting (preferably cationic); are optionally modified with agents such as PEI (polyethylene imine), NMe³, dye, crosslinker, ligands (ligands provide neutral charge); and optionally, are used in combination with a cargo to be delivered to the target.

In certain alternative embodiments, the present invention is directed to cores or particles of a particular size (diameter) ranging from about 0.5 to about 30 nm, about 1 nm to about 30 nm, often about 5 nm to about 25 nm (preferably, less than about 25 nm), often about 10 to about 20 nm, for administration in any useful route. In some embodiments, these cores or particles are often monodisperse and provide colloidally stable compositions. These compositions can be used to target host cells because of enhanced biodistribution/bioavailability of these compositions, and optionally, specific cells, with a wide variety of therapeutic and/or diagnostic agents that exhibit varying release rates at the site of activity.

The cores can be produced in any useful manner. In one instance, cores are formed by templating with a surfactant, a cross-linked micelle, a detergent, or any other useful molecule (see, e.g., Gao F et al., J. Phys. Chem. B. 2009; 113:1796-804; Lin Y S et al., Chem. Mater. 2009; 21(17):3979-86; Carroll N J et al., Langmuir 2009; 25(23):13540-4; and Zhang K et al., J. Am. Chem. Soc. 2013 Feb. 20; 135(7):2427-30). In yet another instance, cores are formed by dendritic growth (see, e.g., Shen D et al., Nano Lett. 2014; 14(2):923-32). In some instances, the cores are formed by expanding a pore, e.g., by use of a swelling agent, such as an alkylbenzene (e.g., 1,3,5-trimethylbenzene or triisopropylbenzene), an alkane (e.g., heptane, decane, or dodecane), a glycol (e.g., poly(propylene glycol)), or a tertiary amine (see, e.g., Kim M H et al., ACS Nano 2011; 5(5):3568-76; and Na H K et al., Small 2012; 8(11):1752-61). In other instances, cores are formed by an aerosol process, such as EISA (see, e.g., Lu Y et al., Nature 1999; 398:223-6; and Durfee P N et al., ACS Nano 2016; 10:8325-45).

Each batch of cores or particles can be characterized in any useful manner, such as by assessment of size and surface charge using dynamic light scattering (DLS) (NIST-NCL PCC-1 and PCC-2), zeta potential measurements, and electron microscopy (NIST-NCL PCC-7 and PCC-15) and verification of low endotoxin contamination per health industry product standards (NCL STE-1.1). Resultant cores can be further processed, such as by modifying core condensation (e.g., by using acidified ethanol for silica), modifying core surface charge (e.g., by use of amine-containing silanes, such as APTES), etc.

The core can be formed of any useful material (e.g., a metal oxide, alum, silica, including mesoporous forms thereof). In particular embodiments, the core is composed of a mesoporous silica nanoparticle (MSN). Exemplary, non-limiting MSNs for use in the present invention are described in Int. Pub. Nos. WO 2015/042268 and WO 2015/042279, each of which is incorporated herein in its entirety.

Spacers

A spacer can be employed to attach a core (e.g., an external surface and/or a pore of the core) to one or more cargos. A spacer can include, for example, a bond (e.g., a covalent bond or a coordination bond), an atom, a molecule, a nucleic acid, a protein, etc. A spacer can be provided as a linking agent, which in turn reacts with a reactive group (e.g., a functional group present on the core or the cargo) to form a bond. Thus, a reacted linking agent can result in a spacer present between the core and the cargo.

A spacer can include a coordination bond. In some instances, the coordination bond includes one or more functional groups that form a bond to a metal (e.g., a divalent metal). Exemplary functional groups include an amino, an amido, a carboxyl, a thiol, a heterocyclyl (e.g., a heteroaryl, imidazolyl, etc.), or an amino acid (e.g., histidine, cysteine, lysine, etc.), as well as chelate forms thereof (e.g., as in iminodiacetic acid or nitriloacetic acid). Exemplary metals include nickel, cobalt, copper, iron, or zinc, as well as cationic forms thereof.

A non-zero length spacer can include a linking group. In some instances, a linking agent (e.g., to form the non-zero length spacer) includes at least two reactive groups and a linking group disposed between the reactive groups. In some instances, a first reactive group forms a bond with the core, and a second reactive group forms a bond with the cargo. The linking group can be any useful chemical moiety (e.g., an optionally substituted alkylene, heteroalkylene, arylene, nucleic acid, peptide, etc.) and can have any useful functionality (e.g., a cleavable moiety, thereby detaching the cargo from the core). The spacer can optionally include a cleavable moiety. Exemplary cleavable moieties include a labile group, a scissile group, etc., including but not limited to a disulfide bond.

The spacer can be provided as a linking agent, which in turn reacts with a reactive group (e.g., a functional group present on the core or the cargo) to form a bond. In some instances, the linking agent is L¹-R^(L)-L², in which R^(L) is a linking group (e.g., any useful chemical group, such as a covalent bond, a nucleic acid sequence, a monomer, etc.) and each of L¹ and L² is, independently, a reactive group (e.g., a functional group that is one of a cross-linker group, a binding group, or a click-chemistry group, such as any described herein), and in which each of L¹ and L² can be the same or different.

FIG. 10A provides an exemplary linking agent L^(1′)-Lk-L^(1″) (compound L1), where Lk is a linking group and where each of L′ and L″ is, independently, a reactive group (e.g., a functional group that is one of a cross-linker group, a binding group, or a click-chemistry group, such as any described herein). In some instances, a reactive group can include a protecting group (e.g., any described herein), which provides a reactive group upon exposure to particular chemical or biological conditions (e.g., an acidic condition, a basic condition, the presence of a protease, etc.).

As seen in FIG. 10A, a first group of the linking agent can be used to react with a core (NP), thereby providing a NP-spacer. A second group of the linking agent can then react with a functional group R¹ of the cargo, thereby providing a NP-spacer-cargo construct. Any useful linking agent and spacer can be employed.

FIG. 10B provided an exemplary spacer present between a core (NP) and the cargo. The spacer -Lk-L″* - - - R¹*, is a linking group (e.g., any described herein), L″* is a reactive group of the linking agent (that underwent a reaction), and R¹ is a second reactive group present on the cargo (that underwent a reaction). The dashed line indicates that the bond can be covalent or non-covalent.

Further spacers are provided in FIG. 10C. In some embodiments, the spacer can include a covalent bond between reacted L″* and reacted X. In one instance, L″*-X can be represented by a reacted sulfone group of the linking agent, a reacted Lys of the cargo, and an alkylene group between the sulfone and Lys. In another instance, two groups on the cargo react with the linking agent, thereby providing a multivalent spacer L″*<(His)₂ between the NP and the cargo. In other embodiments, the spacer can include a non-covalent bond between reacted L″* and reacted X. In one instance, L″*-X can be represented by a chelated Ni²⁺ of the linking agent, a chelated His of the cargo, and a coordination bond between the nickel and His. In another instance, the linking agent provides a reactive group L*, the cargo includes a reactive His, and an intermediate Ni²⁺ is provided to provide a chelating bridge between the linking agent and the cargo.

FIG. 10D provided another exemplary spacer present between a core (NP) and the cargo. The spacer -Lk¹-L^(C)-Lk²-L″* - - - R¹*, in which Lk¹ is a first linking group (e.g., any described herein), L^(C) is a cleavable moiety (e.g., any described herein), Lk² is a second linking group (e.g., any described herein), L″* is a reactive group of the linking agent (that underwent a reaction), and R¹* is a second reactive group present on the cargo (that underwent a reaction). The dashed line indicates that the bond can be covalent or non-covalent. Exemplary linking groups (e.g., for Lk¹ and/or Lk²) includes an optionally substituted alkylene group, an optionally substituted heteroalkylene group, or a poly(ethylene glycol) group.

A cleavable moiety (L^(C)) can include any useful moiety capable of releasing a bound cargo upon exposure to a particular cleaving condition or cleaving agent. In one non-limiting embodiment, the cleavable moiety includes a disulfide group (e.g., —S—S—), in which the cleaving condition includes a reducing condition and the cleaving agent is a reducing agent (e.g., dithiothreitol (DTT), tris(2-carboxyethyl)phosphine (TCEP), or (2S)-2-amino-1,4-dimercaptobutane (DTBA)). In another non-limiting embodiment, the cleavable moiety includes a hydrazone group (e.g., >C═N—NH—), in which the cleaving condition includes an acidic condition and the cleaving agent is an acidic agent (e.g., an acid having a pH less than about 4.5).

A reactive linking group of the linking agent (L″ or L″*) can include any useful moiety, such as one or more anionic moieties (e.g., a chelating anionic moiety, such as a polycarboxylic acid, a carboxylic acid, a carbonate, etc.) and one or more cationic moieties (e.g., a chelated cationic metal, such as a cationic transition metal, including Co²⁺, N²⁺, Fe²⁺, Cu²⁺, or Zn²⁺).

Further exemplary anionic moieties can include those having one or more carboxylic or carbonate moieties, such as iminodiacetic acid (IDA), nitrilotriacetic acid (NTA), ethylenediamine tetraacetic acid (EDTA), diethylenetriaminepentaacetic acid (DTPA), (ethylene glycol-bis(O-aminoethyl ether)-N,N,N′,N′-tetraacetic acid) (EGTA), (1,2-bis(o-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid) (BAPTA), carboxylmethylaspartate (CMA), as well as acidic and basic forms thereof.

A second reactive group present on the cargo (R¹ or R¹*) can include any useful moiety capable of forming a bond with the reactive linking group of the linking agent. In one non-limiting embodiment, the reactive linking group includes a cationic moiety, and the second reactive group present on the cargo is a moiety capable of forming a bond with the cationic moiety. Exemplary second reactive groups include one or more histidine residues located at any useful position of the cargo (e.g., at the N-terminus or the C-terminus for a protein cargo).

FIG. 10E provides an exemplary linking agent L^(1′)-Lk¹-L^(C)-Lk²-L^(1″) (compound L2), where Lk¹ and Lk² are linking groups, where L^(C) is a cleavable moiety, and where each of L^(1′) and L^(1″) is, independently, a reactive group (e.g., a functional group that is one of a cross-linker group, a binding group, or a click-chemistry group, such as any described herein). A first group of the linking agent L2 can be used to react with a core (NP), thereby providing a NP-spacer. A second group of the linking agent can then react with a functional group R¹ of the cargo, thereby providing a NP-spacer-cargo construct. Any useful linking agent and spacer can be employed. Next, as the linker as a cleavable moiety L^(C), the construct can be exposed to a cleaving agent that reacts with L^(C) to provide a released particle (released NP) and a released cargo.

FIG. 11A-11B provides schematics of exemplary reaction schemes for linking agents and spacers. As seen in FIG. 11A, the spacer can include multiple coordination bonds (i), multiple covalent bonds (ii), or a single covalent bond (iii) between the core and the cargo. Such spacers can employ any useful linking agent and reaction schemes. FIG. 11B provides an exemplary reaction scheme in which the linking agent includes a reactive group L″ having an alkene and a sulfone leaving group. The reactive group R¹ of the cargo participates in an addition reaction with L″, thereby providing a single covalent bond present in the spacer. Then, a second reactive group R² of the cargo participated in another addition reaction with the linking agent, thereby providing a second covalent bond present in the spacer. FIG. 11C provides an exemplary reaction scheme in which the linking agent includes a reactive group L″ having an alkene and a sulfone leaving group, and the reactive group R¹ of the cargo participates in an addition reaction to provide a single covalent bond. Other exemplary spacers and linking agents are described in Cong Y et al., Bioconjug. Chem. 2012; 23(2):248-63; Liberatore F A et al., Bioconjug. Chem. 1990; 1(1):36-50; Han D H et al., Nature Commun. 2014; 5(5):5633; and Shen D et al., Nano Lett. 2014; 14(2):923-32, each of which is incorporated herein by reference in its entirety.

Reactive groups can be present on any useful bonding components, such as spacers, linking agents, a surface of the core, and/or a cargo. Pairs of reactive groups can be chosen to facilitate any useful reaction between any bonding components. In one instance, the first bonding component includes a nucleophilic reactive group (e.g., an amino group, a thio group, a hydroxyl group, an anion, etc.), and the second bonding component includes an electrophilic reactive group (e.g., an alkenyl group, an alkynyl group, a carbonyl group, an ester group, an imido group, an epoxide group, an amido group, a carbamido group, a cation, etc.).

Exemplary reactive groups include any chemical group configured to form a bond. In general, a first chemical group reacts with a second chemical group to form a bond (e.g., a covalent bond), in which the first and second chemical groups form a reactive pair.

In one instance, the reactive group is a cross-linker group. In another non-limiting instance, the reactive pair is a cross-linker reaction pair, which includes a first cross-linker group and a second cross-linker group that reacts with that first cross-linker group. Exemplary cross-linker groups and cross-linker reaction pairs include those for forming a covalent bond between a carboxyl group (e.g., —CO₂H) and an amino group (e.g., —NH₂); or between an imido group (e.g., maleimido or succinimido) and a thiol group (e.g., —SH); or between an epoxide group and a thiol group (e.g., —SH); or between an epoxide group and an amino group (e.g., —NH₂); or between an ester group (e.g., —CO₂R, in which R is an organic moiety, such as optionally substituted alkyl, aryl, etc.) and an amino group (e.g., —NH₂); or between an carbamido group (e.g., —NHC(O)Het, where Het is a N-containing heterocyclyl) and an amino group (e.g., —NH₂); or between a phospho group (e.g., —P(O)(OH)₂) and an amino group (e.g., —NH₂), such as 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) and dicyclohexylcarbodiimide (DCC), optionally used with N-hydroxysuccinimide (NHS) and/or N-hydroxysulfosuccinimide (sulfo-NHS). Other cross-linkers include those for forming a covalent bond between an amino group (e.g., —NH₂) and a thymine moiety, such as succinimidyl-[4-(psoralen-8-yloxy)]-butyrate (SPB); a hydroxyl group (e.g., —OH) and a sulfur-containing group (e.g., free thiol, —SH, sulfhydryl, cysteine moiety, or mercapto group), such as p-maleimidophenyl isocyanate (PMPI); between an amino group (e.g., —NH₂) and a sulfur-containing group (e.g., free thiol, —SH, sulfhydryl, cysteine moiety, or mercapto group), such as succinimidyl 4-(p-maleimidophenyl)butyrate (SMPB) and/or succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC); between a sulfur-containing group (e.g., free thiol, —SH, sulfhydryl, cysteine moiety, or mercapto group) and a carbonyl group (e.g., an aldehyde group, such as for an oxidized glycoprotein carbohydrate), such as N-beta-maleimidopropionic acid hydrazide-trifluoroacetic acid salt (BMPH), 3-(2-pyridyldithio)propionyl hydrazide (PDPH), and/or a 3-(2-pyridyldithio)propionyl group (PDP); and between a maleimide-containing group and a sulfur-containing group (e.g., free thiol, —SH, sulfhydryl, cysteine moiety, or mercapto group). Yet other cross-linkers include those for forming a covalent bond between two or more unsaturated hydrocarbon bonds, e.g., such as a reaction of forming a covalent bond between a first alkene group and a second alkene group.

In another instance, the reactive group is a binding group. In another non-limiting instance, the reactive pair is a binding reaction pair, which includes a first binding group and a second binding group that reacts with that first binding group. Exemplary binding groups and binding reaction pairs include those for forming a bond between biotin and avidin, biotin and streptavidin, biotin and neutravidin, desthiobiotin and avidin (or a derivative thereof, such as streptavidin or neutravidin), hapten and an antibody, an antigen and an antibody, a primary antibody and a secondary antibody, and lectin and a glycoprotein.

In yet another instance, the reactive group is a click-chemistry group. In another non-limiting instance, the reactive pair is a click-chemistry reaction pair, which includes a first click-chemistry group and a second click-chemistry group that reacts with that first click-chemistry group. Exemplary click-chemistry groups include, e.g., a click-chemistry group, e.g., one of a click-chemistry reaction pair selected from the group consisting of a Huisgen 1,3-dipolar cycloaddition reaction between an alkynyl group and an azido group to form a triazole-containing spacer; a Diels-Alder reaction between a diene having a 47 electron system (e.g., an optionally substituted 1,3-unsaturated compound, such as optionally substituted 1,3-butadiene, 1-methoxy-3-trimethylsilyloxy-1,3-butadiene, cyclopentadiene, cyclohexadiene, or furan) and a dienophile or heterodienophile having a 27 electron system (e.g., an optionally substituted alkenyl group or an optionally substituted alkynyl group); a ring opening reaction with a nucleophile and a strained heterocyclyl electrophile; and a splint ligation reaction with a phosphorothioate group and an iodo group; and a reductive amination reaction with an aldehyde group and an amino group.

Exemplary reactive groups include an amino (e.g., —NH₂), a thio (e.g., a thioalkoxy group or a thiol group), a hydroxyl, an ester (e.g., an acrylate), an imido (e.g., a maleimido or a succinimido), an epoxide, an isocyanate, an isothiocyanate, an anhydride, an amido, a carbamido (e.g., a urea derivative), an azide, an optionally substituted alkynyl, or an optionally substituted alkenyl.

Exemplary linking groups include any moiety, including any useful subunit, which can be optionally repeated, that provides a spacer having any useful property. Exemplary linking groups include a bond (e.g., a covalent bond), optionally substituted alkylene, optionally substituted heteroalkylene (e.g., poly(ethylene glycol)), optionally substituted arylene, and optionally substituted heteroarylene. Yet other exemplary linking groups are those including an ethylene glycol group, e.g., —OCH₂CH₂—, including a poly(ethylene glycol) (PEG) group —(OCH₂CH₂)_(n)—, a four-arm PEG group (such as C(CH₂O(CH₂CH₂O)_(n)—)₄ or C(CH₂O(CH₂CH₂O)_(n)CH₂—)₄ or C(CH₂O(CH₂CH₂O)_(n)CH₂CH₂—)₄ or C(CH₂O(CH₂CH₂O)_(n)CH₂CH₂NHC(O)CH₂CH₂—)₄C(CH₂O(CH₂CH₂O)_(n)CH₂C(O)O—)₄), an eight-arm PEG group (such as —(OCH₂CH₂)_(n)O [CH₂CHO((CH₂CH₂O)_(n)—)CH₂O]₆(CH₂CH₂O)_(n)— or —CH₂(OCH₂CH₂)_(n)O[CH₂CHO((CH₂CH₂O)_(n)CH₂—)CH₂O]₆(CH₂CH₂O)_(n)CH₂— or —CH₂CH₂(OCH₂CH₂)_(n)O[CH₂CHO((CH₂CH₂O)_(n)CH₂CH₂—)CH₂O]₆(CH₂CH₂O)_(n)CH₂CH₂— or R(O(CH₂CH₂O)_(n)—)₈ or R(O(CH₂CH₂O)_(n)CH₂—)₈ or R(O(CH₂CH₂O)_(n)CH₂CH₂—)₈, in which R includes a tripentaerythritol core), or a derivatized PEG group (e.g., methyl ether PEG (mPEG), a propylene glycol group, etc.); including dendrimers thereof, copolymers thereof (e.g., having at least two monomers that are different), branched forms thereof, start forms thereof, comb forms thereof, etc., in which n is any useful number in any of these (e.g., any useful n to provide any useful number average molar mass M_(n)). Yet other linking groups can include a nucleic acid, a peptide, as well as modified forms thereof.

Exemplary linking agents can include a poly(ethylene glycol) group (e.g., a multivalent poly(ethylene glycol) precursor having a reactive functional group, such as an amino group, an ester group, an acrylate group, a hydroxyl group, a carboxylic acid group, etc.), such as eight arm-PEG amine (8-arm PEG-NH₂, e.g., catalog nos. PSB-811, PSB-812, or PSB-814 available from Creative PEGWorks, Chapel Hill, N.C.) or an eight-arm PEG succinimidyl ester (such as 8-arm PEG succinimidyl NHS ester or 8-arm PEG-SCM (succinimidyl carboxyl methyl ester), e.g., catalog nos. PSB-841, PSB-842, or PSB-844 available from Creative PEGWorks) or an eight-arm PEG vinylsulfone or an eight-arm PEG hydroxyl or a linear PEG thiol or a linear PEG hydroxyl or poly(ethylene glycol diacrylate) (PEG-DA) or triethylene glycol acrylate (TEGA) or 2-carboxyethyl acrylate (CEA) or 2-hydroxyethylacrylate (HEA), as well as copolymers thereof and/or combinations thereof; an amino acid (e.g., a poly(amino acid) precursor or a protein, such as a poly(lysine) precursor, a poly(arginine) precursor, lysozyme, avidin, or albumin); a glycerol group (e.g., a poly(glycerol) precursor); a vinyl group (e.g., a poly(vinyl) precursor or a poly(vinyl alcohol) precursor); a hydroxyacid group (e.g., a poly(lactic acid) precursor, a poly(glycolic acid) precursor, or a poly(lactic-co-glycolic acid) precursor); an acrylate group (e.g., a poly(acrylic acid) precursor or a poly(methacrylic acid) precursor); a silyl ether group (e.g., a poly(silyl ether) precursor); an olefin group (e.g., a poly(acetylene) precursor); and/or an aromatic group (e.g., a poly(pyrrole) precursor, a poly(aniline) precursor, or a poly(thiophene) precursor).

Other exemplary, non-limiting linking agents include 3-aminopropyltrimethoxysilane (3-APTMS); (R,S)-1-(3,4-(methylenedioxy)-6-nitrophenyl)ethyl chloroformate (MenPOC); 1-(6-nitrobenzo[d][1,3]dioxol-5-yl)ethyl (3-(trimethoxysilyl)propyl)carbamate; phenyltrichlorosilane (PTCS); an epoxysilane; sulfo-NHS-acetate; 1-(3-(trimethoxysilyl)propyl)-1H-pyrrole-2,5-dione; 3-glycidoxypropyltrimethoxysilane (3-GPTMS); N-(3-(trimethoxysilyl)propyl)-1H-imidazole-1-carboxamide; N-(6-aminohexyl)-1H-imidazole-1-carboxamide; anhydrides; isocyanotopropyltrimethoxysilane (IPTMS); isocyanates; isothiocyanates; and maleimides.

Yet other non-limiting linking agents include a covalent spacer or a non-covalent spacer. In some embodiments: the spacer may comprise a flexible arm, e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 carbon atoms. Exemplary spacers include BS3 ([bis(sulfosuccinimidyl) suberate]; BS3 is a homobifunctional N-hydroxysuccinimide ester that targets accessible primary amines), NHS/EDC (N-hydroxysuccinimide and N-ethyl-′(dimethylaminopropyl)carbodimide; NHS/EDC allows for the conjugation of primary amine groups with carboxyl groups), sulfo-EMCS ([N-e-Maleimidocaproic acid]hydrazide; sulfo-EMCS are heterobifunctional reactive groups (maleimide and NHS-ester) that are reactive toward sulfhydryl and amino groups), hydrazide (most proteins contain exposed carbohydrates and hydrazide is a useful reagent for linking carboxyl groups to primary amines), and SATA (N-succinimidyl-S-acetylthioacetate; SATA is reactive towards amines and adds protected sulfhydryls groups). Examples of other suitable spacers are succinic acid, Lys, Glu, Asp, a dipeptide such as Gly-Lys, an α-helical spacer (e.g., A(EAAAK).A, where n is 1, 2, 3, 4, or 5), an alkyl chain (e.g., an optionally substituted C₁₋₁₂ alkylene or alkynyl chain), or a polyethylene glycol (e.g., (CH₂CH₂O)_(m), where m is from 1 to 50).

Protecting groups can be employed to protect a reactive group and/or to provide reduced reactivity (e.g., binding) of an agent (e.g., a capture probe). Exemplary protecting groups include any described herein, including optionally substituted aryl groups, a poly(ethylene glycol) group, UV-labile groups, etc.).

Functional groups can be present on a spacer, a core, or a cargo. In addition, a functional group can include any useful chemical group, such as a reactive group or a protecting group. In some instances, the linking agent reacts with a functional group (e.g., present on the cargo or the core), thereby forming an attached spacer that can be further reacted with another functional group.

Cargos

The construct can optionally include any useful cargo, including CRISPR components, as well as other cargos (e.g., associated with the nanoparticle core, with a pore (e.g., by way of a spacer), and/or within the outer layer). Cargos can include a variety of molecules, including peptides, proteins (e.g., including protein complexes, such as a ribonucleoprotein (RNP) complex including a nucleic acid and a protein), nucleic acids (e.g., a plasmid), aptamers, antibodies, small molecule drugs, such as antimicrobials and/or antivirals, carbohydrates, dyes, markers, or any other agent described herein.

The cargo can be characterized by any useful property, such as a second dimension (e.g., that is greater than a first dimension, as described herein). Exemplary dimensions for the cargo include cargo circumference, cargo diameter, cargo length, and cargo width. Exemplary dimensions (e.g., cargo circumference, diameter, length, or width) include of from about 2 nm to about 5000 nm (e.g., from 2 nm to 500 nm, 2 nm to 1000 nm, 2 nm to 2500 nm, 5 nm to 500 nm, 5 nm to 1000 nm, 5 nm to 2500 nm, 5 nm to 5000 nm, 25 nm to 500 nm, 25 nm to 1000 nm, 25 nm to 2500 nm, 25 nm to 5000 nm, 50 nm to 500 nm, 50 nm to 1000 nm, 50 nm to 2500 nm, 50 nm to 5000 nm, 75 nm to 500 nm, 75 nm to 1000 nm, 75 nm to 2500 nm, 75 nm to 5000 nm, 100 nm to 500 nm, 100 nm to 1000 nm, 100 nm to 2500 nm, 100 nm to 5000 nm, 500 nm to 1000 nm, 500 nm to 2500 nm, 500 nm to 5000 nm, 750 nm to 1000 nm, 750 nm to 2500 nm, 750 nm to 5000 nm, 1000 nm to 2500 nm, 1000 nm to 5000 nm, 2500 nm to 5000 nm, or 4000 nm to 5000 nm).

Exemplary cargos include an acidic, basic, and hydrophobic drug (e.g., antiviral agents, antibiotic agents, etc.); a protein (e.g., antibodies, carbohydrates, etc.); a nucleic acid (e.g., DNA, RNA, small interfering RNA (siRNA), minicircle DNA (mcDNA), small hairpin RNA (shRNA), complementary DNA (cDNA), naked DNA, and plasmid, as well as chimeras, single-stranded forms, duplex forms, and multiplex forms thereof and including nucleic acid sequences encoding any of these and including one or more modified nucleic acids); a CRISPR component (e.g., any described herein, including a guiding component (e.g., any described herein), a nuclease, a plasmid, a plasmid that encodes a CRISPR component, a ribonucleoprotein complex, a Cas enzyme or an ortholog or homolog thereof, a guide RNA, as well as a nucleic acid sequence encoding any of these or a complement thereof); a diagnostic/contrast agent, like quantum dots, iron oxide nanoparticles, gadolinium, and indium-111; a small molecule; a carbohydrate; a drug, a pro-drug, a vitamin, an antibody, a protein, a hormone, a growth factor, a cytokine, a steroid, an anticancer agent, a fungicide, an antimicrobial, an antibiotic, an antiviral agent, etc.; a morphogen; a toxin, e.g., a bacterial protein toxin; a peptide, e.g., an antimicrobial peptide; an antigen; an antibody; a detection agent (e.g., a particle, such as a conductive particle, a microparticle, a nanoparticle, a quantum dot, a latex bead, a colloidal particle, a magnetic particle, a fluorescent particle, etc.; or a dye, such as a fluorescent dye, a luminescent dye, a chemiluminescent dye, a colorimetric dye, a radioactive agent, an electroactive detection agent, etc.); a label (e.g., a quantum dot, a nanoparticle, a microparticle, a barcode, a fluorescent label, a colorimetric label, a radio label (e.g., an RF label or barcode), avidin, biotin, a tag, a dye, a marker, an electroactive label, an electrocatalytic label, and/or an enzyme that can optionally include one or more linking agents and/or one or more dyes); a capture agent (e.g., such as a protein that binds to or detects one or more markers (e.g., an antibody or an enzyme), a globulin protein (e.g., bovine serum albumin), a nanoparticle, a microparticle, a sandwich assay reagent, a catalyst (e.g., that reacts with one or more markers), and/or an enzyme (e.g., that reacts with one or more markers, such as any described herein)); as well as combinations thereof.

The nucleic acid can be provided in any useful form, such as RNA, DNA, DNA/RNA hybrids, phage, plasmid, linear forms thereof, concatenated forms thereof, circularized forms thereof, modified forms thereof, single stranded forms thereof, double stranded forms thereof, complements thereof, and encoded forms thereof.

In some instances, the cargo includes a plasmid. The plasmid can encode any useful CRISPR component (e.g., a guiding component or a nuclease). In addition, the plasmid can express any useful polypeptide and/or nucleic acid sequence, including a nuclear localization sequence, a cell penetrating peptide, a targeting peptide, a polypeptide toxin, a small hairpin RNA (shRNA), a small interfering RNA (siRNA), a reporter (e.g., a reporter protein), etc. Additional reporters include polypeptide reporters which may be expressed by plasmids (such as histone-packaged supercoiled DNA plasmids) and include polypeptide reporters such as fluorescent green protein and fluorescent red protein. Reporters pursuant to the present invention are utilized principally in diagnostic applications including diagnosing the existence or progression of a disease state (e.g., diseased tissue) in a subject or patient and/or the progress of therapy in a patient or subject. The plasmid can be of any useful form (e.g., supercoiled and/or packaged plasmid). For instance, the plasmid can be a histone-packaged supercoiled plasmid including a mixture of histone proteins. Additional CRISPR components are described herein.

Exemplary anticancer agents include chenotherapeutic agents, such as an agent selected from the group consisting of microtubule-stabilizing agents, microtubule-disruptor agents, alkylating agents, antimetabolites, epidophyllotoxins, antineoplastic enzymes, topoisomerase inhibitors, inhibitors of cell cycle progression, and platinum coordination complexes, as well as functionalized or modified forms thereof (e.g., including polyethylene glycol (PEG)). These may be selected from the group consisting of everolimus, trabectedin, abraxane, TLK 286, AV-299, DN-101, pazopanib, GSK690693, RTA 744, ON 0910.Na, AZD 6244 (ARRY-142886), AMN-107, TKI-258, GSK461364, AZD 1152, enzastaurin, vandetanib, ARQ-197, MK-0457, MLN8054, PHA-739358, R-763, AT-9263, a FLT-3 inhibitor, a VEGFR inhibitor, an EGFR TK inhibitor, an aurora kinase inhibitor, a PIK-1 modulator, a Bcl-2 inhibitor, an HDAC inhibitor, a c-MET inhibitor, a PARP inhibitor, a Cdk inhibitor, an EGFR TK inhibitor, an IGFR-TK inhibitor, an anti-HGF antibody, a PI3 kinase inhibitors, an AKT inhibitor, a JAK/STAT inhibitor, a checkpoint-1 or 2 inhibitor, a focal adhesion kinase inhibitor, a Map kinase kinase (mek) inhibitor, a VEGF trap antibody, pemetrexed, erlotinib, dasatanib, nilotinib, decatanib, panitumumab, amrubicin, oregovomab, Lep-etu, nolatrexed, azd2171, batabulin, ofatumumab, zanolimumab, edotecarin, tetrandrine, rubitecan, tesmilifene, oblimersen, ticilimumab, ipilimumab, gossypol, Bio 111, 131-I-TM-601, ALT-110, BIO 140, CC 8490, cilengitide, gimatecan, IL13-PE38QQR, INO 1001, IPdR₁ KRX-0402, lucanthone, LY 317615, neuradiab, vitespan, Rta 744, Sdx 102, talampanel, atrasentan, XR 311, romidepsin, ADS- 100380, sunitinib, 5-fluorouracil, vorinostat, etoposide, etoposide phosphate, gemcitabine, doxorubicin, liposomal doxorubicin, 5′-deoxy-5-fluorouridine, vincristine, temozolomide, ZK-304709, seliciclib, PD0325901, AZD-6244, capecitabine, L-glutamic acid, N-[4-[2-(2-amino-4,7-dihydro-4-oxo-1H-pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]benzoyl]-, disodium salt, heptahydrate, camptothecin, PEG-labeled irinotecan, tamoxifen, toremifene citrate, anastrazole, exemestane, letrozole, DES(diethylstilbestrol), estradiol, estrogen, conjugated estrogen, bevacizumab, IMC-1C11, CHIR-258, 3-[5-(methylsulfonylpiperadinemethyl)-indolyl]-quinolone, vatalanib, AG-013736, AVE-0005, the acetate salt of [D-Ser(But)6,Azgly 10] (pyro-Glu-His-Trp-Ser-Tyr-D-Ser(But)-Leu-Arg-Pro-Azgly-NH2 acetate [C₅₉H₈₄N₁₈O₁₄—(C₂H₄O₂)_(x) where x=1 to 2.4], goserelin acetate, leuprolide acetate, triptorelin pamoate, medroxyprogesterone acetate, hydroxyprogesterone caproate, megestrol acetate, raloxifene, bicalutamide, flutamide, nilutamide, megestrol acetate, CP-724714, TAK-165, HKI-272, erlotinib, lapatanib, canertinib, ABX-EGF antibody, erbitux, EKB-569, PKI-166, GW-572016, lonafarnib, BMS-214662, tipifarnib, amifostine, NVP-LAQ824, suberoyl analide hydroxamic acid, valproic acid, trichostatin A, FK-228, SU11248, sorafenib, KRN951, adriamycin, aminoglutethimide, arnsacrine, anagrelide, L-asparaginase, Bacillus Calmette-Guerin (BCG) vaccine, bleomycin, buserelin, busulfan, carboplatin, carmustine, chlorambucil, cisplatin, cladribine, clodronate, cyproterone, cytarabine, dacarbazine, dactinomycin, daunorubicin, diethylstilbestrol, epirubicin, fludarabine, fludrocortisone, fluoxymesterone, flutamide, gemcitabine, hydroxyurea, idarubicin, ifosfamide, imatinib (e.g., including imatinib mesylate), leuprolide, levamisole, lomustine, mechlorethamine, melphalan, 6-mercaptopurine, mesna, methotrexate, mitomycin, mitotane, mitoxantrone, nilutamide, octreotide, oxaliplatin, pamidronate, pentostatin, plicamycin, porfimer, procarbazine, raltitrexed, rituximab, streptozocin, teniposide, testosterone, thalidomide, thioguanine, thiotepa, tretinoin, vindesine, 13-cis-retinoic acid, phenylalanine mustard, uracil mustard, estramustine, altretamine, floxuridine, 5-deooxyuridine, cytosine arabinoside, 6-mecaptopurine, deoxycoformycin, calcitriol, valrubicin, mithramycin, vinblastine, vinorelbine, topotecan, razoxin, marimastat, COL-3, neovastat, BMS-275291, squalamine, endostatin, SU5416, SU6668, EMD121974, interleukin-12, IM862, angiostatin, vitaxin, droloxifene, idoxyfene, spironolactone, finasteride, cimitidine, trastuzumab, denileukin diftitox,gefitinib, bortezimib, paclitaxel, cremophor-free paclitaxel, docetaxel, epithilone B, BMS-247550, BMS-310705, droloxifene, 4-hydroxytamoxifen, pipendoxifene, ERA-923, arzoxifene, fulvestrant, acolbifene, lasofoxifene, idoxifene, TSE-424, HMR-3339, ZK186619, topotecan, PTK787/ZK 222584, VX-745, PD 184352, rapamycin, 40-O-(2-hydroxyethyl)-rapamycin, temsirolimus, AP-23573, RAD001, ABT-578, BC-210, LY294002, LY292223, LY292696, LY293684, LY293646, wortmannin, ZM336372, L-779,450, PEG-filgrastim, darbepoetin, erythropoietin, granulocyte colony-stimulating factor, zolendronate, prednisone, cetuximab, granulocyte macrophage colony-stimulating factor, histrelin, pegylated interferon alfa-2a, interferon alfa-2a, pegylated interferon alfa-2b, interferon alfa-2b, azacitidine, PEG-L-asparaginase, lenalidomide, gemtuzumab, hydrocortisone, interleukin-1, dexrazoxane, alemtuzumab, all-transretinoic acid, ketoconazole, interleukin-2, megestrol, immune globulin, nitrogen mustard, methylprednisolone, ibritgumomab tiuxetan, androgens, decitabine, hexamethylmelamine, bexarotene, tositumomab, arsenic trioxide, cortisone, editronate, mitotane, cyclosporine, liposomal daunorubicin, Edwina-asparaginase, strontium 89, casopitant, netupitant, an NK-1 receptor antagonists, palonosetron, aprepitant, diphenhydramine, hydroxyzine, metoclopramide, lorazepam, alprazolam, haloperidol, droperidol, dronabinol, dexamethasone, methylprednisolone, prochlorperazine, granisetron, ondansetron, dolasetron, tropisetron, pegfilgrastim, erythropoietin, epoetin alfa, and darbepoetin alfa, among others. In some embodiments, the anticancer agent is selected from the group of doxorubicin, melphalan, bevacizumab, dactinomycin, cyclophosphamide, doxorubicin liposomal, amifostine, etoposide, gemcitabine, altretamine, topotecan, cyclophosphamide, paclitaxel, carboplatin, cisplatin, and taxol.

Exemplary antiviral agents (e.g., anti-HIV agents) include, for example, nucleoside reverse transcriptase inhibitors (NRTI), non-nucleoside reverse transcriptase inhibitors (NNRTI), protease inhibitors, fusion inhibitors, among others, exemplary compounds of which may include, for example, 3TC (Lamivudine), AZT (Zidovudine), (−)-FTC, ddI (Didanosine), ddC (zalcitabine), abacavir (ABC), tenofovir (PMPA), D-D4FC (Reverset), D4T (Stavudine), Racivir, L-FddC, L-FD4C, NVP (Nevirapine), DLV (Delavirdine), EFV (Efavirenz), SQVM (Saquinavir mesylate), RTV (Ritonavir), IDV (Indinavir), SQV (Saquinavir), NFV (Nelfinavir), APV (Amprenavir), LPV (Lopinavir), fusion inhibitors such as T20, among others, fuseon and mixtures thereof, including anti-HIV compounds presently in clinical trials or in development. Exemplary anti-HBV agents include, for example, hepsera (adefovir dipivoxil), lanivudine, entecavir, telbivudine, tenofovir, emtricitabine, clevudine, valtoricitabine, amdoxovir, pradefovir, racivir, BAM 205, nitazoxanide, UT 231-B, Bay 41-4109, EHT899, zadaxin (thymosin alpha-1) and mixtures thereof. Anti-HCV agents include, for example, interferon, pegylated intergeron, ribavirin, NM 283, VX-950 (telaprevir), SCH 50304, TMC435, VX-500, BX-813, SCH503034, R1626, ITMN-191 (R7227), R7128, PF-868554, TT033, CGH-759, GI 5005, MK-7009, SIRNA-034, MK-0608, A-837093, GS 9190, ACH-1095, GSK625433, TG4040 (MVA-HCV), A-831, F351, NS5A, NS4B, ANA598, A-689, GNI-104, IDX102, ADX184, GL59728, GL60667, PSI-7851, TLR9 Agonist, PHX1766, SP-30 and mixtures thereof.

Other exemplary antiviral agents include broad spectrum antiviral agents, antibodies, small molecule antiviral agents, antiretroviral agents, etc. Further non-limiting antiviral agents include abacavir, ACH-3102, acyclovir (acyclovir), acyclovir, adefovir, amantadine, amprenavir, ampligen, arbidol, asunaprevir, atazanavir, atripla, balavir, BCX4430, boceprevir, brincidofovir, brivudine, cidofovir, clevudine, combivir, cytarabine, daclatasvir, dasabuvir, deleobuvir, dolutegravir, darunavir, delavirdine, didanosine, docosanol, edoxudine, efavirenz, elbasvir, emtricitabine, enfuvirtide, entecavir, ecoliever, faldaprevir, famciclovir, favipiravir, fomivirsen, fosamprenavir, foscarnet, fosfonet, ganciclovir, grazoprevir, ibacitabine, imunovir, idoxuridine, imiquimod, indinavir, interferon type III, interferon type II, interferon type I, interferon, interferon alfa 2b, lamivudine, laninamivir, ledipasvir (with or without sofosbuvir), lopinavir, loviride, maraviroc, moroxydine, methisazone, MK-3682, MK-8408, nelfinavir, nevirapine, nexavir, novir, ombitasvir (with or without paritaprevir and/or ritonavir), oseltamivir (Tamiflu), paritaprevir, peginterferon alfa-2a, penciclovir, peramivir, pleconaril, podophyllotoxin, raltegravir, resiquimod, ribavirin, rifampicin, rimantadine, ritonavir, pyramidine, samatasvir, saquinavir, simeprevir, sofosbuvir, stavudine, taribavirin, tecovirimat (ST-246), telaprevir, telbivudine, tenofovir, tenofovir disoproxil, tipiracil, tipranavir, trifluridine (with or without tipiracil), trizivir, tromantadine, truvada, umifenovir, valaciclovir (Valtrex), valganciclovir, vicriviroc, vidarabine, viramidine, zalcitabine, zanamivir (Relenza), zidovudine, including prodrugs, salts, and/or combinations thereof.

Exemplary antibiotics or antibacterial agents include gentamicin, kanamycin, neomycin, netilmicin, tobramycin, paromomycin, spectinomycin, geldanamycin, herbimycin, rifaximin, streptomycin, ertapenem, doripenem, imipenem/cilastatin, meropenem, cefadroxil, cefazolin, cephalothin, cephalexin,cefaclor, cefamandole, cefoxitin, cefprozil, cefuroxime, cefixime, cefdinir, cefditoren, cefoperazone cefotaxime, cefpodoxime, ceftazadime, ceftibuten, ceftizoxime ceftriaxone, cefepime, ceftaroline fosamil, ceftobiprole, teicoplanin, vancomycin, telavancin, daptomycin, oritavancin, WAP-8294A, azithromycin, clarithromycin, dirithromycin, erythromycin, roxithromycin, telithromycin, spiramycin, clindamycin, lincomycin, aztreonam, furazolidone, nitrofurantoin, oxazolidonones, linezolid, posizolid, radezolid, torezolid, amoxicillin, ampicillin, azlocillin, carbenicillin, cloxacillin dicloxacillin, flucloxacillin, mezlocillin, methicillin, nafcillin, oxacillin, penicillin G, penicillin V, piperacillin, temocillin, ticarcillin, amoxicillin/clavulanate, ampicillin/sulbactam, piperacillin/tazobactam, ticarcillin/clavulanate, bacitracin, colistin, polymyxin B, ciprofloxacin, enoxacin, gatifloxacin, gemifloxacin, levofloxacin, lomefloxacin, moxifloxacin, nalidixic acid, norfloxacin, ofloxacin, trovafloxacin, grepafloxacin, sparfloxacin, mafenide, sulfacetamide, sulfadiazine, sulfadimethoxine, sulfamethizole, sulfamethoxazole, sulfasalazine, sulfisoxazole, trimethoprim-sulfamethoxazole, sulfonamidochrysoidine, demeclocycline, doxycycline, vibramycin minocycline, tigecycline, oxytetracycline, tetracycline, clofazimine, capreomycin, cycloserine, ethambutol, rifampicin, rifabutin, rifapentine, arsphenamine, chloramphenicol, fosfomycin, fusidic acid, metronidazole, mupirocin, platensimycin, quinupristin/dalfopristin, thiamphenicol, tigecycline, and tinidazole and combinations thereof.

CRISPR Components

CRISPR components include any employing a nucleic acid sequence capable of recruiting a CRISPR-associated (Cas) protein to achieve genetic modification. An exemplary CRISPR component includes those having a trans-acting CRISPR RNA (tracrRNA) and CRISPR RNA (crRNA) fused into a single, synthetic ‘guide RNA’ that directs a Cas nuclease (e.g., Cas9) to virtually any desired DNA sequence (see, e.g., FIG. 12). The synthetic guide RNA (gRNA) can include at least three different portions: a first portion including the tracrRNA sequence, a second portion including the crRNA sequence, and a third portion including a targeting portion or a genomic specific sequence (gsRNA) that binds to a desired genomic target sequence (e.g., genomic target DNA sequence, including a portion or a strand thereof). The chimeric tracrRNA-crRNA sequence facilitates binding and recruitment of the endonuclease (e.g., Cas9), and the gsRNA sequence provides site-specificity to the target nucleic acid, thereby allowing Cas9 to selectively introduce site-specific breaks in the target.

In any embodiment herein, the cargo can include a CRISPR component. Exemplary CRISPR components can include a guide RNA, a Cas enzyme, and a nucleic acid sequence (e.g., a plasmid) encoding any of these. Yet other exemplary CRISPR components are shown in FIGS. 12, 13A-13C, 14A-14H, 15, 16A-16C, 17, 18, and 19, including, as applicable, a nucleic acid sequence encoding any of these (e.g., a nucleic acid sequence encoding any polypeptide sequence therein, such as SEQ ID Nos: 110-117 or a fragment thereof), a polypeptide generated by any nucleic acid sequence therein, as well as a complement of any nucleic acid sequence therein (e.g., a nucleic acid sequence that is a complement of any one of SEQ ID Nos: 20-32, 40-54, 60-65, 80-93, 100-103, or a fragment thereof).

In particular embodiments, the particle can include one or more CRISPR components (e.g., associated with or within a pore of the core (e.g., by way of a spacer), associated with a surface of the core, and/or within the outer layer). FIG. 12 and FIG. 13A-13C shows exemplary CRISPR components.

This CRISPR/Cas system can be adapted to control genetic expression in targeted manner, such as, e.g., by employing synthetic, non-naturally occurring constructs that use crRNA nucleic acid sequences, tracrRNA nucleic acid sequences, and/or Cas polypeptide sequences, as well as modified forms thereof.

One CRISPR component includes a guiding component. In general, the guiding component includes a nucleic acid sequence (e.g., a single polynucleotide) that includes at least two portions: a targeting portion, which is a nucleic acid sequence that imparts specific targeting to the target genomic locus (e.g., a guide RNA or gRNA); and an interacting portion, which is another nucleic acid sequence that binds to a nuclease (e.g., a Cas endonuclease). In some instances, the interacting portion includes two particular sequences that bind the nuclease, e.g., a short crRNA sequence attached to the guide nucleic acid sequence; and a tracrRNA sequence attached to the crRNA sequence. Exemplary targeting CRISPR components include a minicircle DNA vector optimized for in vivo expression.

Another CRISPR component includes a nuclease (e.g., that binds the targeting nucleic acid sequence). The nuclease CRISPR component can either be an enzyme, or a nucleic acid sequence that encodes for that enzyme. Exogenous endonuclease (e.g., Cas9) can be encoded by a cargo stored within the construct. Any useful nuclease can be employed, such as Cas9 (e.g., SEQ ID NO:110), as well as nickase forms and deactivated forms (e.g., SEQ ID NO:111) thereof (e.g., including one or more mutations, such as D10A, H840A, N₈₅₄A, and N₈₆₃A in SEQ ID NO:110 or in an amino acid sequence sufficiently aligned with SEQ ID NO:110), including nucleic acid sequences that encode for such nuclease. Pathogen-directed and host-directed CRISPR components (e.g., guiding components and/or nuclease), as well as minicircle DNA vectors that encode Cas and guiding components can be developed. The nuclease can be configured to bind the target sequence and/or cleave the target sequence.

Non-limiting examples of nucleases are described in FIG. 14A-14H. In some embodiments, a vector comprises a regulatory element operably linked to an enzyme-coding sequence encoding a nuclease (e.g., a CRISPR enzyme, such as a Cas protein). Non-limiting examples of Cas proteins include Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csn1 and Csx12), Cas10, Csy1, Csy2, Csy3, Cse1, Cse2, Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csbl, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1, Csx15, Csf1, Csf2, Csf3, Csf4, homologs thereof, or modified versions thereof. These enzymes are known; for example, the amino acid sequence of S. pyogenes Cas9 protein may be found in the SwissProt database under accession number Q99ZW2. In some embodiments, the unmodified CRISPR enzyme has DNA cleavage activity, such as Cas9. In some embodiments the CRISPR enzyme is Cas9, and may be Cas9 from S. pyogenes or S. pneumoniae. In some embodiments, the CRISPR enzyme directs cleavage of one or both strands at the location of a target sequence, such as within the target sequence and/or within the complement of the target sequence. In some embodiments, the CRISPR enzyme directs cleavage of one or both strands within about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 50, 100, 200, 500, or more base pairs from the first or last nucleotide of a target sequence.

The nuclease may be a Cas9 homolog or ortholog. In some embodiments, the nuclease is codon-optimized for expression in a eukaryotic cell. In some embodiments, the nuclease directs cleavage of one or two strands at the location of the target sequence. In some embodiments, the nuclease lacks DNA strand cleavage activity. In some embodiments, the first regulatory element is a polymerase III promoter. In some embodiments, the second regulatory element is a polymerase II promoter.

Any useful Cas protein or complex can be employed. Exemplary Cas proteins or complexes include those involved in Type I, Type II, or Type III CRISPR/Cas systems, including but not limited to the CRISPR-associated complex for antiviral defense (Cascade, including a RAMP protein), Cas3 and/or Cas 7 (e.g., for Type I systems, such as Type I-E systems), Cas9 (formerly known as Csn1 or Csx12, e.g., such as in Type II systems), Csm (e.g., in Type III-A systems), Cmr (e.g., in Type III-B systems), Cas10 (e.g., in Type III systems), as well as subassemblies or sub-components thereof and assemblies including such Cas proteins or complexes. Additional Cas proteins and complexes are described in Makarova K S et al., “Evolution and classification of the CRISPR-Cas systems,” Nat. Rev. Microbiol. 2011; 9:467-77, which is incorporated herein by reference in its entirety.

In some embodiments, a vector encodes a CRISPR enzyme that is mutated to with respect to a corresponding wild-type enzyme such that the mutated CRISPR enzyme lacks the ability to cleave one or both strands of a target polynucleotide containing a target sequence. For example, an aspartate-to-alanine substitution (D10A) in the RuvC I catalytic domain of Cas9 from S. pyogenes converts Cas9 from a nuclease that cleaves both strands to a nickase (cleaves a single strand). Other examples of mutations that render Cas9 a nickase include, without limitation, H840A, N854A, and N₈₆₃A. In aspects of the invention, nickases may be used for genome editing via homologous recombination. In some instances, the Cas protein includes a modification of one of more of D10A, H840A, N854A, and N863A in SEQ ID NO:110 or in an amino acid sequence sufficiently aligned with SEQ ID NO:110.

As a further example, two or more catalytic domains of Cas9 (RuvC I, RuvC II, and RuvC III) may be mutated to produce a mutated Cas9 substantially lacking all DNA cleavage activity. In some embodiments, a D10A mutation is combined with one or more of H840A, N854A, or N863A mutations to produce a Cas9 enzyme substantially lacking all DNA cleavage activity. In some embodiments, a CRISPR enzyme is considered to substantially lack all DNA cleavage activity when the DNA cleavage activity of the mutated enzyme is less than about 25%, 10%, 5%, 1%, 0.1%, 0.01%, or lower with respect to its non-mutated form. Other mutations may be useful; where the Cas9 or other CRISPR enzyme is from a species other than S. pyogenes, mutations in corresponding amino acids may be made to achieve similar effects.

In some embodiments, the guiding component comprises a modification or sequence that provides for an additional desirable feature (e.g., modified or regulated stability; subcellular targeting; tracking, e.g., a fluorescent label; a binding site for a protein or protein complex; etc.). Non-limiting examples include: a short motif (referred to as the protospacer adjacent motif (PAM)); a 5′ cap (e.g., a 7-methylguanylate cap (m7G)); a 3′ polyadenylated tail (i.e., a 3′ poly(A) tail); a riboswitch sequence (e.g., to allow for regulated stability and/or regulated accessibility by proteins and/or protein complexes); a stability control sequence; a sequence that forms a dsRNA duplex (i.e., a hairpin)); a modification or sequence that targets the RNA to a subcellular location (e.g., nucleus, mitochondria, chloroplasts, and the like); a modification or sequence that provides for tracking (e.g., direct conjugation to a fluorescent molecule, conjugation to a moiety that facilitates fluorescent detection, a sequence that allows for fluorescent detection, etc.); a modification or sequence that provides a binding site for proteins (e.g., proteins that act on DNA, including transcriptional activators, transcriptional repressors, DNA methyltransferases, DNA demethylases, histone acetyltransferases, histone deacetylases, and the like); and combinations thereof.

A guiding component and a nuclease can form a complex (i.e., bind via non-covalent interactions). The guiding component provides target specificity to the complex by comprising a nucleotide sequence that is complementary to a sequence of a target sequence. The nuclease of the complex provides the site-specific activity. In other words, the nuclease is guided to a target sequence (e.g., a target sequence in a chromosomal nucleic acid; a target sequence in an extrachromosomal nucleic acid, e.g., an episomal nucleic acid, a minicircle, etc.; a target sequence in a mitochondrial nucleic acid; a target sequence in a chloroplast nucleic acid; a target sequence in a plasmid; etc.) by virtue of its association with the protein-binding segment (e.g., the interacting portion) of the guiding component.

In some embodiments, the guiding component comprises two separate nucleic acid molecules (e.g., a separate targeting portion and a separate interacting portion; a separate first portion and a separate second portion; or a separate targeting portion-first portion that is covalently bound and a separate second portion). In other embodiments, the guiding component is a single nucleic acid molecule including a covalent bond or a linker between each separate portion (e.g., a targeting portion covalently linked to an interacting portion).

FIG. 12 shows an exemplary CRISPR component that includes a guiding component 90 to bind to the target sequence 97, as well as a nuclease 98 (e.g., a Cas nuclease or an endonuclease, such as a Cas endonuclease) that interacts with the guiding component and the target sequence. As can be seen, the guiding component 90 includes a targeting portion 94 configured to bind to the target sequence 97 of a genomic sequence 96 (e.g., a target sequence having substantially complementarity with the genomic sequence or a portion thereof). In this manner, the targeting portion confers specificity to the guiding component, thereby allowing certain target sequences to be activated, inactivated, and/or modified.

The guiding component 90 also includes an interacting portion 95, which in turn is composed of a first portion 91, a second portion 92, and a linker 93 that covalently links the first and second portions. The interacting portion 95 is configured to recruit the nuclease (e.g., a Cas nuclease) in proximity to the site of the target sequence. Thus, the interacting portion includes nucleic acid sequences that provide preferential binding (e.g., specific binding) of the nuclease. Once in proximity, the nuclease 98 can bind and/or cleave the target sequence or a sequence in proximity to the target sequence in a site-specific manner.

The first portion, second portion, and linker can be derived in any useful manner. In one instance, the first portion can include a crRNA sequence, a consensus sequence derived from known crRNA sequences, a modified crRNA sequence, or an entirely synthetic sequence known to bind a Cas nuclease or determined to competitively bind a Cas nuclease when compared to a known crRNA sequence. Exemplary sequences for a first portion are described in FIG. 15 (SEQ ID NOs:20-32). Another exemplary sequence for a first portion is 5′-GUUUUAGAGCUA-3′ (SEQ ID NO:70). In some embodiments, the first portion is a nucleic acid sequence having at least 80% sequence identity (e.g., at least 85%, 90%, 95%, or 99% sequence identity) to any one of SEQ ID NOs:20-32 and 70 or a complement of any of these, or a fragment thereof (e.g., having a length of about 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, or more nucleotides).

In some embodiments, the first portion is a crRNA sequence that exhibits at least 50%, 60%, 70%, 80%, 90%, 95%, or 99% of sequence complementarity to any one of SEQ ID NOs:20-32 and 70. In other embodiments, the first portion is a fragment (e.g., having a length of about 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, or more nucleotides) of a crRNA sequence that exhibits at least 50%, 60%, 70%, 80%, 90%, 95%, or 99% of sequence complementarity to any one of SEQ ID NOs:20-32 and 70.

In another instance, the second portion can include a tracrRNA sequence, a consensus sequence derived from known tracrRNA sequences, a modified tracrRNA sequence, or an entirely synthetic sequence known to bind a Cas nuclease or determined to competitively bind a Cas nuclease when compared to a known tracrRNA sequence. Exemplary sequences for a second portion are described in FIG. 16A-16C (SEQ ID NOs:40-54) and in FIG. 17 (SEQ ID NOs:60-65). Another exemplary sequence for a second portion is 5′-UAGCAAGUUAAAA UAAGGCUAGUCCG-3′ (SEQ ID NO:71).

In some embodiments, the second portion is a nucleic acid sequence having at least 80% sequence identity (e.g., at least 85%, 90%, 95%, or 99% sequence identity) to any one of SEQ ID NOs:40-54, 60-65, and 71 or a complement of any of these, or a fragment thereof (e.g., having a length of about 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, or more nucleotides).

In some embodiments, the second portion is a tracrRNA sequence that exhibits at least 50%, 60%, 70%, 80%, 90%, 95%, or 99% of sequence complementarity to any one of SEQ ID NOs:40-54, 60-65, and 71. In other embodiments, the second portion is a fragment (e.g., having a length of about 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, or more nucleotides) of a tracrRNA sequence that exhibits at least 50%, 60%, 70%, 80%, 90%, 95%, or 99% of sequence complementarity to any one of SEQ ID NOs:40-54, 60-65, and 71.

The linker can be any useful linker (e.g., including one or more transcribable elements, such as a nucleotide or a nucleic acid, or including one or more chemical linkers). Further, the linker can be derived from a fragment of any useful tracrRNA sequence (e.g., any described herein). The first and second portions can interact in any useful manner. For example, the first portion can have a sequence portion that is sufficiently complementary to a sequence portion of the second portion, thereby facilitating duplex formation or non-covalent bonding between the first and second portion. In another example, the second portion can include a first sequence portion that is sufficiently complementary to a second sequence portion, thereby facilitating hairpin formation within the second portion. Further CRISPR components are described in FIG. 13A-13C.

In another embodiment, the guiding component has a structure of A-L-B, in which A includes a first portion (e.g., any one of SEQ ID NOs:20-32 and 70, or a fragment thereof), L is a linker (e.g., a covalent bond, a nucleic acid sequence, a fragment of any one of SEQ ID NOs:40-54, 60-65, and 71, or any other useful linker or spacer described herein), and B is a second portion (e.g., any one of SEQ ID NOs:40-54, 60-65, and 71, or a fragment thereof) (FIG. 18). In another embodiment, the guiding component is a sequence having at least 80% sequence identity (e.g., at least 85%, 90%, 95%, or 99% sequence identity) to any one SEQ ID NOs:80-93, or a fragment thereof.

In yet another embodiment, the guiding component is a sequence that exhibits at least 50%, 60%, 70%, 80%, 90%, 95%, or 99% of sequence complementarity to any one SEQ ID NOs:100-103, or a fragment thereof (FIG. 19). In another embodiment, the guiding component is a sequence having at least 80% sequence identity (e.g., at least 85%, 90%, 95%, or 99% sequence identity) to any one SEQ ID NOs:100-103, or a fragment thereof.

The CRISPR components can be provided in any useful form. In some embodiments, the CRISPR component includes ds plasmid DNA, which is modified to express RNA and/or a protein. In other embodiments, the CRISPR component is supercoiled and/or packaged (e.g., within a complex, such as those containing histones, lipids (e.g., lipoplexes), proteins (e.g., cationic proteins), cationic carrier, nanoparticles (e.g., gold or metal nanoparticles), etc.), which may be optionally modified with a nuclear localization sequence (e.g., a peptide sequence incorporated or otherwise crosslinked into histone proteins, which comprise the histone-packaged supercoiled plasmid DNA). Other exemplary histone proteins include H1, H2A, H2B, H3 and H4, e.g., in a ratio of 1:2:2:2:2 with optional nuclear localization sequences (e.g., any described herein, such as SEQ ID NOs:9-12).

The CRISPR component can include any useful promoter sequence(s), expression control sequence(s) that controls and regulates the transcription and translation of another DNA sequence, and signal sequence(s) that encodes a signal peptide. The promoter sequence can include a DNA regulatory region capable of binding RNA polymerase in a cell and initiating transcription of a downstream (3′ direction) coding sequence. For purposes of defining the present invention, the promoter sequence is bounded at its 3′ terminus by the transcription initiation site and extends upstream (5′ direction) to include the minimum number of bases or elements necessary to initiate transcription at levels detectable above background. Within the promoter sequence will be found a transcription initiation, as well as protein binding domains (consensus sequences) responsible for the binding of RNA polymerase. Eukaryotic promoters will often, but not always, contain “TATA” boxes and “CAT” boxes. Prokaryotic promoters contain Shine-Dalgamo sequences in addition to the −10 and −35 consensus sequences.

In addition, the CRISPR components can be formed from any useful combination of one or more nucleic acids (or a polymer of nucleic acids, such as a polynucleotide). Exemplary nucleic acids or polynucleotides of the invention include, but are not limited to, ribonucleic acids (RNAs), deoxyribonucleic acids (DNAs), threose nucleic acids (TNAs), glycol nucleic acids (GNAs), peptide nucleic acids (PNAs), locked nucleic acids (LNAs, including LNA having a 3-D-ribo configuration, α-LNA having an α-L-ribo configuration (a diastereomer of LNA), 2′-amino-LNA having a 2′-amino functionalization, and 2′-amino-α-LNA having a 2′-amino functionalization) or hybrids, chimeras, or modified forms thereof. Exemplary modifications include any useful modification, such as to the sugar, the nucleobase, or the internucleoside linkage (e.g., to a linking phosphate/to a phosphodiester linkage/to the phosphodiester backbone). One or more atoms of a pyrimidine nucleobase may be replaced or substituted with optionally substituted amino, optionally substituted thiol, optionally substituted alkyl (e.g., methyl or ethyl), or halo (e.g., chloro or fluoro). In certain embodiments, modifications (e.g., one or more modifications) are present in each of the sugar and the internucleoside linkage. Modifications according to the present invention may be modifications of ribonucleic acids (RNAs) to deoxyribonucleic acids (DNAs), threose nucleic acids (TNAs), glycol nucleic acids (GNAs), peptide nucleic acids (PNAs), locked nucleic acids (LNAs) or hybrids thereof). Additional modifications are described herein.

Toxicity of CRISPR components, to the host, can be minimized in any useful manner.

For instance, toxicity can result from protocells or carriers due to expression of Cas9 products or immune responses. Specifically, the lifetime of CRISPR components in the cell can be controlled by adding features that are stabilized or destabilized with cellular proteases, by inducing expression only under a microbial or viral promoter, and by using guiding components with modified backbones (e.g., 2-OMe) to minimize immune recognition.

Resistance to CRISPR components can be minimized. Any single antibiotic or antiviral countermeasure is prone to the development of resistance, so pathogens will likely mutate around individual guiding component targets. However, we will prevent the development of resistance by targeting orthogonal mechanisms via multiplexed guiding components in combination with current antivirals/antimicrobials.

Off-target mutations or genetic modification can be minimized. For instance, bioinformatic guiding component design programs can be used to determine minimal effective CRISPR component doses. If needed, the nickase version of Cas9 can be employed.

The CRISPR component can be employed to target any useful nucleic acid sequence (e.g., present in the host's genomic sequence and/or the pathogen's genomic sequence). In one instance, the target sequence can include a sequence present in the host's genomic sequence in order, e.g., activate, inactive, or modify expression of factor or proteins within the host's cellular machinery. For instance, the target sequence can bind to one or more genomic sequences for an immunostimulatory protein that, upon expression, would enhance the immune response by the host to an infection. Pathogens are known to down-regulate proteins that would otherwise assist in recognizing non-self protein motifs. Thus, in another instance, the target sequence can bind to one or more regulator proteins and enhance their transcription and expression. In yet another instance, one or more polypeptides may be up-regulated, as compared to the normal basal rate, and such up-regulation may be modified by the presence of the pathogen. Accordingly, the target sequence can be employed to bind to one or more up-regulated polypeptides in order to inactivate or repress transcription/expression of those polypeptides.

An exemplary target sequence (e.g., in a host or subject) includes, without limitation, a nucleic acid sequence encoding an immunostimulatory protein, a cluster of differentiation protein, a cell surface protein, a pathogen receptor protein (e.g., a pathogen recognition receptor, such as TLR9), a glycoprotein (e.g., granulocyte-colony stimulating factor), a cytokine (e.g., interferon or transforming growth factor beta (TGF-beta)), a pattern recognition receptor protein, a hormone (e.g., a prostaglandin), or a helicase enzyme.

In yet another instance, the target sequence can be employed to activate, inhibit, and/or modify a target sequence (e.g., associated with the presence of a pathogen, a tumor, etc.). For instance, the target sequence can be configured to activate one or more target sequences encoding proteins that promote programmed cell death or apoptosis (e.g., of the pathogen or of particular tissue types, such as metastatic growths, tumors, lesions, etc.). For instance, the target sequence can be configured to inactivate or modify one or more target sequences encoding proteins that are suppressed by the pathogen. Exemplary target sequence (e.g., in a pathogen) includes, without limitation, a nucleic acid sequence encoding a virulence factor (e.g., a lipase, a protease, a nuclease (e.g., a DNAse or an RNase), a hemolysin, a hyaluronidase, an immunoglobulin protease, an endotoxin, or an exotoxin), a cell surface protein (e.g., an adhesion), an envelope protein (e.g., a phospholipid, a lipopolysaccharide, a lipoprotein, or a polysaccharide), a glycoprotein, a polysaccharide protein, a transmembrane protein (e.g., an invasin), or a regulatory protein.

The CRISPR component can be employed to activate the target sequence (e.g., the Cas polypeptide can include one or more transcriptional activation domains, which upon binding of the Cas polypeptide to the target sequence, results in enhanced transcription and/or expression of the target sequence), inactivate the target sequence (e.g., the Cas polypeptide can bind to the target sequence, thereby inhibiting expression of one or more proteins encoded by the target sequence; the Cas polypeptide can introduce double-stranded or single-stranded breaks in the target sequence, thereby inactivating the gene; or the Cas polypeptide can include one or more transcriptional repressor domains, which upon binding of the Cas polypeptide to the target sequence, results in reduced transcription and/or expression of the target sequence), and/or modify the target sequence (e.g., the Cas polypeptide can cleave the target sequence of the pathogen and optionally inserts a further nucleic acid sequence).

Any useful transcriptional activation domains can be employed (e.g., VP64, VP16, HIV TAT, or a p65 subunit of nuclear factor KB). In particular, such activation domains are useful when employed with a deactivated or modified form of the Cas polypeptide with minimized cleavage activity. In this way, specific recruitment of the Cas polypeptide to the target sequence is enabled by the interacting portion of the target component, and transcriptional activity is controlled by the activation domains.

Further, any useful transcriptional repressor domains can be employed (e.g., a Kruppel-associated box domain, a SID domain, an Engrailed repression domain (EnR), or a SID4X domain). In particular, such repressor domains can be employed with a deactivated or modified form of the Cas polypeptide with minimized cleavage activity or with an active Cas polypeptide with retained endonuclease activity.

A guiding component may be selected to target any target sequence. In some embodiments, the target sequence is a sequence within a genome of a host (e.g., a host cell) or a pathogen (e.g., a pathogen cell). In some embodiments, the guiding component is about or more than about 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 75, or more nucleotides in length. In some embodiments, a guiding component is less than about 75, 50, 45, 40, 35, 30, 25, 20, 15, 12, or fewer nucleotides in length. The ability of a guiding component to direct sequence-specific binding of a CRISPR complex to a target sequence may be assessed by any suitable assay. For example, the components of a CRISPR system sufficient to form a CRISPR complex, including the guiding component to be tested, may be provided to a host cell having the corresponding target sequence, such as by transfection with vectors encoding the components of the CRISPR sequence, followed by an assessment of preferential cleavage within the target sequence, such as by Surveyor assay. Similarly, cleavage of a target sequence may be evaluated in a test tube by providing the target sequence, components of a CRISPR complex, including the guiding component to be tested and a control guiding component different from the test guiding component, and comparing binding or rate of cleavage at the target sequence between the test and control guiding component reactions. Other assays are possible, and will occur to those skilled in the art.

Outer Layer

The present invention relates to an outer layer disposed around a core. In particular embodiments, the outer layer can include a lipid layer (e.g., supported by the surface of the core) that can optionally include one or more moieties (e.g., one or more targeting ligands). In other embodiments, the outer layer can include a polymer layer (e.g., supported by the surface of the core) that can optionally include one or more moieties (e.g., one or more targeting ligands).

The outer layer can be characterized in any useful manner, such as by the thickness of the outer layer (e.g., of from about 5 nm to about 50 nm), the number of layers within the outer layers (e.g., two, three, four, five, six, seven, or more lipid and/or polymer layers within the outer layer), and/or the net charge of the outer layer (e.g., a net non-negative charge, such as a net positive charge; or as determined by the composition of the lipid layer, such as one formed by use of a liposome formulation having more than about 20 mol. % of a cationic lipid, such as any herein (e.g., DOTAP)).

The outer layer can include any useful component, including a cationic lipid, a pegylated lipid, a zwitterionic lipid, a sterol (e.g., a cholesterol), and/or a polymer. The lipid layer can include any useful lipid or combination of lipids or component, such as one or more lipids selected from the group of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), 1,2-dioleoyl-sn-glycero-3-[phosphor-L-serine] (DOPS), 1,2-dioleoyl-3-trimethylammonium-propane (18:1 DOTAP), 1,2-dioleoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (DOPG), 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE), 1,2-distearoyl-sn-glycero-3-phosphoethanolamine (DSPE), 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine (SOPC), 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000] (18:1 PEG-2000 PE), 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000] (16:0 PEG-2000 PE), 1-oleoyl-2-[12-[(7-nitro-2-1,3-benzoxadiazol-4-yl)amino]lauroyl]-sn-glycero-3-phosphocholine (18:1-12:0 NBD PC), 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy-(polyethylene glycol)-2000] (DSPE-PEG₂₀₀₀), 1-palmitoyl-2-{12-[(7-nitro-2-1,3-benzoxadiazol-4-yl)amino]lauroyl}-sn-glycero-3-phosphocholine (16:0-12:0 NBD PC), a sterol (e.g., cholesterol, desmosterol, diplopterol, cholestanol, cholic acid, 12-deoxycholic acid, 7-deoxycholic acid, or a derivative thereof, such as cholesterol sulfate), and mixtures thereof and conjugated forms thereof (e.g., conjugated to PEG moieties, peptides, polypeptides, including immunogenic peptides, proteins and antibodies, and nucleic acids (e.g., RNA and DNA) by way of a covalent bond or by way of any useful linker or spacer (e.g., any described herein).

Exemplary polymers can include a polymer including polyethylene glycol (PEG) or polyethylene oxide (PEO) (e.g., a PEG-polyester), a copolymer (e.g., a diblock copolymer, such as an amphiphilic diblock copolymer). Non-limiting polymers include a PEG-lactic acid polymer (PEG-LA, e.g., poly(ethyleneglycol)-b-poly(lactic acid) copolymer or PEG-b-poly(D,L-lactic acid)); a polycarbonate-polyglutamic acid polymer (PC-PGA, e.g., poly(trimethylene carbonate)-b-poly(glutamic acid); a poly(lactic acid) (PLA, e.g., methoxy poly(ethylene glycol)-Gly-Phe-Leu-Gly-Phe-poly(D,L-lactide), PEG-PLA, or maleimide-PEG-PLA); a poly(butadiene) (PBD, e.g., PEO-b-PBD or PEG-PBD); a poly(caprolactone) (PCL, e.g., PEG-PCL, PEO-PCL, PEG-b-poly(F-caprolactone), mPEG-poly(F-caprolactone), α-carboxyl PEG-poly(3-caprolactone)/PEG-PLA, or PEO-b-poly(γ-methyl-3-caprolactone)); and a PEG- or PEO-polypeptide (e.g., PEG-b-poly(2-hydroxyethyl aspartamide) substituted with octadecyl chains, poly(carboxyl ethylene glycol-γ-glutamate)-co-poly(distearin-γ-glutamate), or poly(ethylene glycol)-γ-glutamate)-co-poly (distearin-γ-glutamate)).

The outer layer can be a hybrid layer (e.g., including one or more lipids and one or more polymers). Exemplary hybrid layers can include a lipid (e.g., any described herein), an optional sterol, and a polymer (e.g., any described herein, such as a polymer including PEG or PEO).

Exemplary, non-limiting sterols include cholesterol (e.g., from ovine wool or from plant sources), campestanol, campesterol, cholestanol, cholestenone, desmosterol, 7-dehydrodesmosterol, dehydroepiandrosterone (DHEA), desmosterol, diosgenin, FF-MAS (14-demethyl-14-dehydrolanosterol), lanosterol, lathosterol, pregnenolone, sitostanol, sitosterol, stigmasterol, zymosterol, zymostenol, zymosterone, as well as derivatives thereof, such as sulfates thereof, esters thereof, stereoisomers thereof, deuterated forms thereof, sulfonated forms thereof, phosphorylated forms thereof, unsaturated forms thereof, keto forms thereof, oxidized forms thereof, an oxysterol thereof, PEGylated forms thereof (e.g., cholesterol-(polyethylene glycol-600)), or substituted forms thereof (e.g., having one or more hydroxyl, epoxy, alkyl, phospho, and/or halo, such as fluoro).

Cores, lipids, polymers, and cargos can be PEGylated with a variety of polyethylene glycol-containing compositions as described herein. PEG molecules can have a variety of lengths and molecular weights and include, but are not limited to, PEG 200, PEG 1000, PEG 1500, PEG 2000, PEG 4600, PEG 5000, PEG 10,000, PEG-peptide conjugates or combinations thereof.

In one instance, the lipid layer includes DOPE and DOTAP. In another instance, the lipid layer includes a zwitterionic lipid (e.g., DOPC, DPPC, DOPE, DPPE, DSPE, DLPC, DMPC, POPC, or SOPC) with an optional PEG (e.g., PEG, PEG-2000 PE, PEG conjugated to DOPE, PEG conjugated to DPPE, PEG conjugated to DSPE, etc.).

In yet another instance, the lipid layer includes DOTAP and cholesterol in a 1:1 molar ratio. In another instance, the lipid layer includes PEG. In yet another instance, the lipid layer includes DOPE. In one instance, the lipid layer includes DOTAP in combination with about 4 mol. % DOPE, about 47 mol. % cholesterol, and about 2 mol. % DSPE-PEG₂₀₀₀. In another instance, the lipid layer includes about 10 to about 50 mol. % DOTAP, about 40 to 50 mol. % cholesterol, about 0 to 40 mol. % DOPE, and about 1 to 5 mol. % of a PEGylated lipid.

The outer layer can be formed by employing any useful lipid formulation. A non-limiting exemplary formulation can include the following: about 1 mol. % to about 5 mol. % of a PEGylated lipid (e.g., from 1 mol. % to 3 mol. %, 1 mol. % to 4 mol. %, 2 mol. % to 3 mol. %, 2 mol. % to 4 mol. %, 2 mol. % to 5 mol. %, 3 mol. % to 4 mol. %, or 3 mol. % to 5 mol. %); about 30 mol. % to about 60 mol. % of a sterol (e.g., from 30 mol. % to 50 mol. %, 35 mol. % to 50 mol. %, 35 mol. % to 60 mol. %, 40 mol. % to 50 mol. %, 40 mol. % to 60 mol. %, 45 mol. % to 50 mol. %, 45 mol. % to 60 mol. %, 50 mol. % to 60 mol. %, or 55 mol. % to 60 mol. %); about 20 mol. % to about 90 mol. % of a cationic lipid (e.g., from 20 mol. % to 30 mol. %, 20 mol. % to 40 mol. %, 20 mol. % to 50 mol. %, 20 mol. % to 60 mol. %, 20 mol. % to 70 mol. %, 20 mol. % to 80 mol. %, 30 mol. % to 40 mol. %, 30 mol. % to 50 mol. %, 30 mol. % to 60 mol. %, 30 mol. % to 70 mol. %, 30 mol. % to 80 mol. %, 30 mol. % to 90 mol. %, 40 mol. % to 50 mol. %, 40 mol. % to 60 mol. %, 40 mol. % to 70 mol. %, 40 mol. % to 80 mol. %, 40 mol. % to 90 mol. %, 50 mol. % to 60 mol. %, 50 mol. % to 70 mol. %, 50 mol. % to 80 mol. %, 50 mol. % to 90 mol. %, 60 mol. % to 70 mol. %, 60 mol. % to 80 mol. %, 60 mol. % to 90 mol. %, 70 mol. % to 80 mol. %, 70 mol. % to 90 mol. %, or 80 mol. % to 90 mol. %); and about 0 mol. % to about 40 mol. % of a zwitterionic lipid (e.g., 0 mol. % to 3 mol. %, 0 mol. % to 5 mol. %, 0 mol. % to 7 mol. %, 0 mol. % to 10 mol. %, 0 mol. % to 15 mol. %, 0 mol. % to 20 mol. %, 0 mol. % to 25 mol. %, 0 mol. % to 30 mol. %, 0 mol. % to 35 mol. %, 3 mol. % to 5 mol. %, 3 mol. % to 7 mol. %, 3 mol. % to 10 mol. %, 3 mol. % to 15 mol. %, 3 mol. % to 20 mol. %, 3 mol. % to 25 mol. %, 3 mol. % to 30 mol. %, 3 mol. % to 35 mol. %, 3 mol. % to 40 mol. %, 7 mol. % to 10 mol. %, 7 mol. % to 15 mol. %, 7 mol. % to 20 mol. %, 7 mol. % to 25 mol. %, 7 mol. % to 30 mol. %, 7 mol. % to 35 mol. %, 73 mol. % to 40 mol. %, 10 mol. % to 15 mol. %, 10 mol. % to 20 mol. %, 10 mol. % to 25 mol. %, 10 mol. % to 30 mol. %, 10 mol. % to 35 mol. %, 10 mol. % to 40 mol. %, 15 mol. % to 20 mol. %, 15 mol. % to 25 mol. %, 15 mol. % to 30 mol. %, 15 mol. % to 35 mol. %, 15 mol. % to 40 mol. %, 20 mol. % to 25 mol. %, 20 mol. % to 30 mol. %, 20 mol. % to 35 mol. %, 20 mol. % to 40 mol. %, 25 mol. % to 30 mol. %, 25 mol. % to 35 mol. %, 25 mol. % to 40 mol. %, 30 mol. % to 35 mol. %, 30 mol. % to 40 mol. %, or 35 mol. % to 40 mol. %), or salts of any of these (e.g., pharmaceutically acceptable salts, such as any described herein).

In particular embodiments, the ratio of the sterol to the cationic lipid is about 1:1. In other embodiments, the lipid formulation includes about 2% of the PEGylated lipid. In yet other embodiments, the lipid formulation includes about 30 mol. % to about 60 mol. % of the cationic lipid.

The lipid formulation can include any useful lipid or component. Exemplary PEGylated lipids (e.g., a lipid having a poly(ethylene glycol moiety)) include PEGylated DSPE (e.g., 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[amino(polyethylene glycol)-X] (DSPE X) or N-[carbonyl-2′,3′-bis(methoxypolyethyleneglycol X)]-1,2-distearoyl-sn-glycero-3-phosphoethanolamine (DSPE-2arm PEGX)), PEGylated phosphoethanolamine (PE) (e.g., 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-X] (18:1 PEGX PE), 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-X](18:0 PEGX PE), 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-X] (14:0 PEGX PE), or 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-5000] (16:0 PEGX PE)), PEGylated DPPE (e.g., N-(carbonyl-methoxypolyethyleneglycol X)-1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine), PEGylated DMPE (e.g., N-(carbonyl-methoxypolyethyleneglycol X)-1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine), PEGylated DPG (e.g., 1,2-dipalmitoyl-sn-glycerol, methoxypolyethylene glycol), PEGylated DSG (e.g., 1,2-distearoyl-sn-glycerol, methoxypolyethylene glycol), PEGylated DOG (e.g., 1,2-dioleoyl-sn-glycerol, methoxypolyethylene glycol), or PEGylated DMG (e.g., 1,2-dimyristoyl-sn-glycerol, methoxypolyethylene glycol), where X indicates an approximate weight average molecular weight (Mw) or approximate number average molecular weight (Mn), and where can be X 500, 3000, 2000, 1000, 750, 550, or 350.

Exemplary sterols include, e.g., cholesterol, a derivative thereof, or any described herein. Exemplary zwitterionic lipids include DOPC, DPPC, DOPE, DPPE, POPC, DLPC, DSPC, DMPC, SOPC, or any described herein.

Exemplary cationic lipids include 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP), 1,2-stearoyl-3-trimethylammonium-propane (18:0 TAP), 1,2-dipalmitoyl-3-trimethylammonium-propane (16:0 TAP), 1,2-dimyristoyl-3-trimethylammonium-propane (14:0 TAP), 1,2-di-O-octadecenyl-3-trimethylammonium propane (DOTMA), N1-[2-((1S)-1-[(3-aminopropyl)amino]-4-[di(3-amino-propyl)amino]butylcarboxamido)ethyl]-3,4-di[oleyloxy]-benzamide (MVL5), ethylphosphocholine (ethyl PC) (e.g., 1,2-dimyristoleoyl-sn-glycero-3-ethylphosphocholine, 1-palmitoyl-2-oleoyl-sn-glycero-3-ethylphosphocholine, 1,2-dioleoyl-sn-glycero-3-ethylphosphocholine, 1,2-distearoyl-sn-glycero-3-ethylphosphocholine, 1,2-dipalmitoyl-sn-glycero-3-ethylphosphocholine, 1,2-dimyristoyl-sn-glycero-3-ethylphosphocholine, or 1,2-dilauroyl-sn-glycero-3-ethylphosphocholine), dimethyldioctadecylammonium (DDAB), 1,2-dipalmitoyl-sn-glycero-O-ethyl-3-phosphocholine (EDPPC), or any described herein.

The outer layer of the particle can be composed of lipids, polymers, and/or components in an amount similar to that provided by the lipid formulation. For instance, an exemplary lipid formulation comprising about 47 mol. % of a cationic lipid can provide a lipid layer (for a construct) that comprises 47 mol. % of that cationic lipid. Thus, any composition provided for a lipid formulation herein also provides a composition for the lipid layer.

Targeting Ligands

The construct can include one or more cell targeting species, cell receptor ligands, cell penetrating peptides, fusogenic peptides, and/or targeting peptides. Such species can be included within the cargo, configured to be expressed by a plasmid of the cargo, located within the outer layer, and/or provided by an external surface of the outer layer (e.g., provided by the outer lipid layer). The composition of the outer layer can include one or more components that facilitate ligand orientation, maximize cellular interaction, provide lipid stability, and/or confer enhanced cellular entry.

In some instances, the targeting ligand can be a cell penetration peptide, a fusogenic peptide, or an endosomolytic peptide, which are peptides that aid a particle in translocating across a lipid bilayer, such as a cellular membrane or endosome lipid bilayer of the host cell. In one embodiment, the targeting ligand is optionally crosslinked onto a lipid layer surface of the outer layer.

Endosomolytic peptides are a sub-species of fusogenic peptides as described herein. Representative and preferred electrostatic cell penetration (fusogenic) peptides include an 8 mer polyarginine (NH₂—RRRRRRRR-COOH, SEQ ID NO:1), among others known in the art, which are included in or on particles in order to enhance the penetration of into cells. Representative endosomolytic fusogenic peptides (“endosomolytic peptides”) include H5WYG peptide (NH₂-GLFHAIAHFIHGGWHGLIHGWYGGC-COOH, SEQ ID NO:2), RALA peptide (NH₂—WEARLARALARALARHLARALARALRAGEA-COOH, SEQ ID NO:3), KALA peptide (NH₂-WEAKLAKALAKALAKHLAKALAKALKAGEA-COOH), SEQ ID NO:4), GALA (NH₂-WEAALAEALAEALAEHLAEALAEALEALAA-COOH, SEQ ID NO:5) and INF7 (NH₂-GLFEAIEGFIENGWEGMIDGWYG-COOH, SEQ ID NO:6), or fragments thereof, among others. In one instance, the targeting ligand includes an amino acid sequence having at least 80% sequence identity (e.g., at least 85%, 90%, 95%, or 99% sequence identity) to any one of SEQ ID NOs:1-6, or a fragment thereof.

Proteins gain entry into the nucleus through the nuclear envelope. Yet other ligands can include a nuclear localization sequence (NLS), e.g., NH₂-GNQSSNFGPMKGGNFGGRSSGPY GGGGQYFAKPRNQGGYGGC-COOH (SEQ ID NO:9), RRMKWKK (SEQ ID NO:10), PKKKRKV (SEQ ID NO:11), and KR[PAATKKAGQA]KKKK (SEQ ID NO:12), the NLS of nucleoplasmin, a prototypical bipartite signal comprising two clusters of basic amino acids, separated by a spacer of about 10 amino acids. Numerous other nuclear localization sequences are well known in the art. See, for example, LaCasse E C et al., “Nuclear localization signals overlap DNA- or RNA-binding domains in nucleic acid-binding proteins,” Nucl. Acids Res. 1995; 23:1647-56; Weis, K, “Importins and exportins: how to get in and out of the nucleus,” [published erratum appears in Trends Biochem. Sci. 1998 July; 23(7):235] Trends Biochem. Sci. 1998; 23:185-9; and Cokol M et al., EMBO Rep. 2000 Nov. 15; 1(5): 411-5, each of which is incorporated herein by reference in its entirety.

Preferred ligands which may be used to target cells include peptides, affibodies, and antibodies (including monoclonal and/or polyclonal antibodies). In certain embodiments, targeting ligands selected from the group consisting of Fcγ from human IgG (which binds to Fcγ receptors on macrophages and dendritic cells), human complement C3 (which binds to CR1 on macrophages and dendritic cells), ephrin B2 (which binds to EphB4 receptors on alveolar type II epithelial cells), SP94 peptide (which binds to unknown receptor(s) on hepatocyte-derived cells), and MET receptor binding peptide. Exemplary, non-limiting SP94 peptides include SP94 free peptide (H₂N-SFSIILTPILPL-COOH, SEQ ID NO:126), a SP94 peptide modified with C-terminal Cys for conjugation (H₂N-SFSIILTPILPLGGC-COOH, SEQ ID NO:127), and a further modified SP94 peptide (H₂N-SFSIILTPILPLEEEGGC-COOH, SEQ ID NO:128). Exemplary MET binding peptides include ASVHFPP (SEQ ID NO:121), TATFWFQ (SEQ ID NO:122), TSPVALL (SEQ ID NO:123), IPLKVHP (SEQ ID NO:124), and WPRLTNM (SEQ ID NO:125).

Other exemplary targeting ligands include poly-L-arginine, including (R)_(n), where 6<n<12, such as an R¹² peptide (e.g., RRRRRRRRRRRR (SEQ ID NO:210)) or an R⁹ peptide (e.g., RRRRRRRRR (SEQ ID NO:211)); a poly-histidine-lysine, such as a (KH)₉ (e.g., KHKHKHKHKHKHKHKHKH (SEQ ID NO:212)); a Tat protein or derivatives and fragments thereof, such as RKKRRQRRR (SEQ ID NO:213), GRKKRRQRRRPQ (SEQ ID NO:214), GRKKRRQRRR (SEQ ID NO:215), GRKKRRQRRRPPQ (SEQ ID NO:216), YGRKKRRQRRR (SEQ ID NO:217), and RKKRRQRRRRKKRRQRRR (SEQ ID NO:218); a Cady protein or derivatives and fragments thereof, such as Ac-GLWRALWRLLRSLWRLLWRA-cysteamide (SEQ ID NO:219); a penetratin protein or derivatives and fragments thereof, such as RQIKIWFQNRRMKWKKGG (SEQ ID NO:220), RQIRIWFQNRRMRWRR (SEQ ID NO:221), and RQIKIWFQNRRMKWKK (SEQ ID NO:222); an antitrypsin protein or derivatives and fragments thereof, such as CSIPPEVKFNKPFVYLI (SEQ ID NO:223); a temporin protein or derivatives and fragments thereof, such as FVQWFSKFLGRIL-NH₂ (SEQ ID NO:224); a MAP protein or derivatives and fragments thereof, such as KLALKLALKALKAALKLA (SEQ ID NO:225); a RW protein or derivatives and fragments thereof, such as RRWWRRWRR (SEQ ID NO:226); a pVEC protein or derivatives and fragments thereof, such as LLIILRRRIRKQAHAHSK (SEQ ID NO:227); a transportan protein or derivatives and fragments thereof, such as GWTLNSAGYLLGKIN LKALAALAKKIL (SEQ IDNO:228); a MPG protein or derivatives and fragments thereof, such as GALFLGFLGAAGSTMGAWSQPKKKRKV (SEQ ID NO:229); a Pep protein or derivatives and fragments thereof, such as KETWWETWWTEWSQPKKKRKV (SEQ ID NO:230), Ac-KETWWETWWTEWSQPKKKRKV-cysteamine (SEQ ID NO:231), and WKLFKKILKVL-amide (SEQ ID NO:232); a Bp100 protein or derivatives and fragments thereof, such as KKLFKKILKYL (SEQ ID NO:233) and KKLFKKILKYL-amide (SEQ ID NO:234); a maurocalcine protein or derivatives and fragments thereof, such as GDC(acm)LPHLKLC (SEQ ID NO:235); a calcitonin protein or derivatives and fragments thereof, such as LGTYTQDFNKFHTFPQTAIGVGAP (SEQ ID NO:236); a neurturin protein or derivatives and fragments thereof, such as GAAEAAARVYDLGLRRLRQRRRLRRERVRA (SEQ ID NO:237); and a human P1 protein or derivatives and fragments thereof, such as MGLGLHLLVLAAALQGAWSQPKKKRKV (SEQ ID NO:238).

In one instance, the targeting ligand includes an amino acid sequence having at least 80% sequence identity (e.g., at least 85%, 90%, 95%, or 99% sequence identity) to any one of SEQ ID NOs:10-12 and 210-238 or a fragment thereof (e.g., having a length of about 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, or more amino acids).

Particle Characteristics and Surface Properties

The construct can be characterized by any useful characteristic (e.g., overall charge, dimension, dispersity, etc.). In some embodiments, one or more optional targeting ligands can be present in or on an outer layer. The particle can have any useful dimension, such as diameter, circumference, length, width, height, etc. Exemplary values for dimensions include, without limitation, greater than about 10 nm (e.g., greater than about 20 nm, 30 nm, 40 nm, 50 nm, 60 nm, 70 nm, 80 nm, 90 nm, 100 nm, 125 nm, 150 nm, 200 nm, 300 nm, 500 nm, 750 nm, 1 m, 2 m, 5 m, 10 m, 20 m, or more) or of from about 2 nm to 500 nm (e.g., from 2 nm to 50 nm, 2 nm to 100 nm, 2 nm to 150 nm, 2 nm to 200 nm, 2 nm to 300 nm, 2 nm to 400 nm, 10 nm to 50 nm, 10 nm to 100 nm, 10 nm to 150 nm, 10 nm to 200 nm, 10 nm to 300 nm, 10 nm to 400 nm, 10 nm to 500 nm, 20 nm to 50 nm, 20 nm to 100 nm, 20 nm to 150 nm, 20 nm to 200 nm, 20 nm to 300 nm, 20 nm to 400 nm, 20 nm to 500 nm, 50 nm to 100 nm, 50 nm to 150 nm, 50 nm to 200 nm, 50 nm to 300 nm, 50 nm to 400 nm, 50 nm to 500 nm, 100 nm to 150 nm, 100 nm to 200 nm, 100 nm to 300 nm, 100 nm to 400 nm, 100 nm to 500 nm, 150 nm to 200 nm, 150 nm to 300 nm, 150 nm to 400 nm, 150 nm to 500 nm, 200 nm to 300 nm, 200 nm to 400 nm, or 200 nm to 500 nm).

In particular embodiments, a plurality of particles is monodisperse, such as by having a polydispersity index (PdI) that is less than about 0.2 or by having a PdI that is of from about 0.05 to about 0.2 (e.g., from 0.05 to 0.1, 0.05 to 0.15, 0.1 to 0.15, 0.1 to 0.2, or 0.15 to 0.2). In some embodiments, the monodisperse particles range in a size of from about 20 nm to about 300 nm (e.g., from 50 nm (+/−10 nm) to 150 nm (+/−15 nm)). In other embodiments, the particle (or a plurality of particles) has a charge (or a net charge) that is near neutral (e.g., a zeta potential of from about +5 mV to −5 mV).

In certain alternative embodiments, the present invention is directed to particles of a particular size (diameter) ranging from about 0.5 to about 30 nm, about 1 nm to about 30 nm, often about 5 nm to about 25 nm (preferably, less than about 25 nm), often about 10 to about 20 nm, for administration via intravenous, intramuscular, intraperitoneal, retro-orbital, and subcutaneous injection routes. These particles can be monodisperse and provide colloidally stable compositions.

The surface properties of the particle can be optimized in any useful manner. For instance, the outer layer can have an appropriate charge (e.g., approximately net neutral charge), can include appropriate targeting ligands to promote their cell-specific binding and internalization, and can include useful ligand (e.g., to promote endosomal escape or nuclear localization within host cells).

Any useful ligand can be employed. The type and density of targeting ligands can be optimized to enhance uptake by the target. Exemplary ligands include a peptide that binds to ephrin B2, which we identified using phage display, to target Vero cells; Fcγ to target THP-1 cells and primary alveolar macrophages; the ‘GE11’ peptide (see, e.g., Li Z et al., FASEB J 2006; 19: 1978-85) to target A549 cells and primary alveolar epithelial cells; the ‘SP94’ peptide (see, e.g., Lo A et al., Molec. Cancer Therap. 2008; 7:579-89) to target HepG2 cells and primary hepatocytes; human complement C3, which binds to receptors on macrophages and dendritic cells; or the ‘H5WYG’ peptide, which ruptures the membranes of acidic intracellular vesicles via the ‘proton sponge’ mechanism (see, e.g., Moore N M et al., J. Gene. Med. 2008 10: 1134-49).

Other ligands include a peptide (e.g., a peptide zip code or a cell penetrating peptide), an endosomolytic peptide, an antibody (including fragments thereof), affibodies, a carbohydrate, an aptamer, a cluster of differentiation (CD) protein, or a self-associated molecular pattern (SAMP) (e.g., as described in Lambris J D et al., Nat. Rev. Microbiol. 2008; 6(2):132; and Poon I K H, Cell Death Differ. 2010; 17:381-97, each of which is incorporated herein by reference in its entirety). Exemplary CD proteins include CD47 (OMIM Entry No. 601028, a marker of self that allows RBC to avoid phagocytosis), CD59 (OMIM Entry No. 107271, a marker that prevents lysis by complement), C1 inhibitor (C1INH, OMIM Entry No. 606860, a marker that suppresses activation of the host's complement system), CD200 (OMIM Entry No. 155970, an immunosuppressive factor), CD55 (OMIM Entry No. 125240, a marker that inhibits the complement cascade), CD46 (OMIM Entry No. 120920, a marker that inhibits the complement cascade), and CD31 (OMIM Entry No. 173445, an adhesion regulator and a negative regulator of platelet-collagen interactions). Each recited OMIM Entry is incorporated herein by reference in its entirety.

Any other useful ligand can be employed, such as those identified by the ‘BRASIL’ (Biopanning and Rapid Analysis of Selective Interactive Ligands) method (see, e.g., Giordano R J et al., Nat. Med. 2001; 7:1249-53; Giordano R J et al., Proc. Natl Acad. Sci. USA 2010; 107(11):5112-7; and Kolonin M G et al., Cancer Res. 2006; 66:34-40) to identify novel targeting peptides and single-chain variable fragments (scFvs) via phage display (see, e.g., Giordano R J et al., Chem. Biol. 2005; 12:1075-83; Giordano R J et al., Proc. Natl Acad. Sci. USA 2010; 107(11):5112-7; Kolonin M G et al., Cancer Res. 2006; 66:34-40; Tonelli R R et al., PLoS Negl. Dis. 2010; 4:e864; Lionakis M S et al., Infect. Immun. 2005; 73:7747-58; and Barbu E M et al., PLoS Pathog. 2010; 6:e1000726).

Compositions and Formulations

The present constructs can be formulated in any useful manner. For instance, the formulation can be optimized for subcutaneous (SC), intranasal (IN), aerosol, intravenous (IV), intramuscular (IM), intraperitoneal (IP), oral, topical, transdermal, or retro-orbital delivery. Any useful dosages can be employed within the formulations. Exemplary dosages include, e.g., 200 mg/kg. The formulation or composition can include a plurality of particles (e.g., an effective amount thereof) and an optional pharmaceutically acceptable excipient (e.g., any described herein).

In some instances, the pharmaceutical composition includes a population of particles (e.g., any described herein) in an amount effective for modulating or modifying a target gene within a subject in combination with a pharmaceutically acceptable carrier, additive, or excipient. In other instances, the composition further includes a drug, a therapeutic agent, etc., which is not disposed as cargo within the particle.

The composition can be formulated in any useful manner with a plurality of particles. Such formulations can be included with any useful medium, excipient (e.g., lactose, saccharide, carbohydrate, mannitol, leucine, PEG, trehalose, etc.), additive, propellant, solution (e.g., aqueous solution, such as a buffer), additive, preservative, carrier (e.g., aqueous saline, aqueous dextrose, glycerol, or ethanol), binder (e.g., saccharide, cellulose preparation, starch paste, or methyl cellulose), filler, or disintegrator.

Pharmaceutical compositions according to the present invention include an effective population of constructs herein formulated to effect an intended result (e.g., immunogenic result, therapeutic result and/or diagnostic analysis, including the monitoring of therapy) formulated in combination with a pharmaceutically acceptable carrier, additive or excipient. The particles within the population of the composition may be the same or different depending upon the desired result to be obtained. Pharmaceutical compositions according to the present invention may also comprise an addition bioactive agent or drug, such as an antibiotic or antiviral agent.

Formulations and compositions containing the particles according to the present invention may take the form of liquid, solid, semi-solid or lyophilized powder forms, such as, for example, solutions, suspensions, emulsions, sustained-release formulations, tablets, capsules, powders, suppositories, creams, ointments, lotions, aerosols, patches or the like, preferably in unit dosage forms suitable for simple administration of precise dosages.

Methods for preparing such dosage forms are known or apparent to those skilled in the art; for example, see Remington's Pharmaceutical Sciences (17th Ed., Mack Pub. Co., 1985). The composition to be administered will contain a quantity of the selected compound in a pharmaceutically effective amount for therapeutic use in a biological system, including a patient or subject according to the present invention.

Methods

The constructs herein can be employed in any useful manner. The present particles can be adapted to recognize the target and, if needed, deliver the one or more cargos to treat that target. Exemplary targets include a cell, a pathogen, an organ (e.g., dermis, vasculature, lymphoid tissue, liver, lung, spleen, kidneys, heart, brain, bone, muscle, etc.), a cellular target (e.g., targets of the subject, such as a human subject, including host tissue, host cytoplasm, host nucleus, etc., in any useful cell, such as e.g., hepatocytes, alveolar epithelial cells, and innate immune cells, etc.); as well as targets for exogenous cells and organisms, such as extracellular and/or intracellular components of a pathogen, e.g., bacteria), a molecular target (e.g., within the subject or the exogenous cell/organism, such as pathogen DNA, host DNA, pathogen RNA, pathogen proteins, surface proteins or carbohydrates of any subject or exogenous cell), etc.

In one instance, the particle is employed to target a host (e.g., a subject), a pathogen, or both (e.g., thereby treating the subject and/or the target). Exemplary pathogens include a bacterium, such as Bacillus (e.g., B. anthracis), Enterobacteriaceae (e.g., Salmonella, Escherichia coli, Yersinia pestis, Klebsiella, and Shigella), Yersinia (e.g., Y. pestis or Y. enterocolitica), Staphylococcus (e.g., S. aureus), Streptococcus, Gonorrheae, Enterococcus (e.g., E. faecalis), Listeria (e.g., L. monocytogenes), Brucella (e.g., B. abortus, B. melitensis, or B. suis), Vibrio (e.g., V. cholerae), Corynebacterium diphtheria, Pseudomonas (e.g., P. pseudomallei or P. aeruginosa), Burkholderia (e.g., B. mallei or B. pseudomallei), Shigella (e.g., S. dysenteriae), Rickettsia (e.g., R. rickettsii, R. prowazekii, or R. typhi), Francisella tularensis, Chlamydia psittaci, Coxiella burnetii, Mycoplasma (e.g., M. mycoides), etc.; mycotoxins, mold spores, or bacterial spores such as Clostridium botulinum and C. perfringens; a virus, including DNA or RNA viruses, such as Adenoviridae (e.g., adenovirus), Arenaviridae (e.g., Machupo virus), Bunyaviridae (e.g., Hantavirus or Rift Valley fever virus), Coronaviridae, Orthomyxoviridae (e.g., influenza viruses), Filoviridae (e.g., Ebola virus and Marburg virus), Flaviviridae (e.g., Japanese encephalitis virus, hepatitis C virus, and Yellow fever virus), Hepadnaviridae (e.g., hepatitis B virus), Herpesviridae (e.g., herpes simplex viruses, herpesvirus, cytomegalovirus, Epstein-Barr virus, or varicella zoster viruses), Papillomaviridae (e.g., papilloma viruses), Papovaviridae (e.g., papilloma viruses), Paramyxoviridae (e.g., respiratory syncytial virus, measles virus, mumps virus, or parainfluenza virus), Parvoviridae, Picornaviridae (e.g., polioviruses and hepatitis A virus), Polyomaviridae, Poxviridae (e.g., variola viruses or vaccinia virus), Reoviridae (e.g., rotaviruses), Retroviridae (e.g., human T cell lymphotropic viruses (HTLV) and human immunodeficiency viruses (HIV)), Rhabdoviridae (e.g., rabies virus), and Togaviridae (e.g., encephalitis viruses, yellow fever virus, and rubella virus)); a protozoon, such as Cryptosporidium parvum, Encephalitozoa, Plasmodium, Toxoplasma gondii, Acanthamoeba, Entamoeba histolytica, Giardia lamblia, Trichomonas vaginalis, Leishmania, or Trypanosoma (e.g., T. brucei and T. Cruzi); a helminth, such as cestodes (tapeworms), trematodes (flukes), or nematodes (roundworms, e.g., Ascaris lumbricoides, Trichuris trichiura, Necator americanus, or Ancylostoma duodenale); a parasite (e.g., any protozoa or helminths described herein); or a fungus, such as Aspergilli, Candidae, Coccidioides immitis, and Cryptococci. Other pathogens include a multi-drug resistant (MDR) pathogen, such as MDR forms of any pathogen described herein. Additional pathogens are described in Cello J et al., Science 2002; 297:1016-8; Gibson D G et al., Science 2010; 329:52-6; Jackson R J et al., J. Virol. 2001; 75:1205-10; Russell C A et al., Science 2012; 336:1541-7; Tumpey T M et al., Science 2005; 310:77-80; and Weber N D et al., Virology 2014; 454-455c:353-61, each of which is incorporated herein by reference in its entirety.

The constructs of the invention can be employed to treat any useful disease that would benefit from genetic knock-out of a known protein. For instance, the particles can be employed to treat a subject from a disease correlated with the presence of that known protein (e.g., a known protein expressed within the subject or within a pathogen infecting that subject). Other diseases include a genetic disorder (e.g., Huntington's disease, hemophilia, sickle cell anemia, metabolic disorders, etc.), in which expression of a known protein is correlated with the disease or its symptoms.

The constructs can be employed to transform a subject (e.g., by genetically modifying a target gene within the subject by employing a CRISPR component configured to bind to that target gene). Thus, in one instance, the particle can be configured to bind to a target sequence in a genomic sequence of the subject in order to modulate that target sequence. Modulation can include activating, inactivating, deactivating, and/or modifying expression or activity of the target sequence. For example, the cargo can bind to the target sequence, e.g., thereby inhibiting expression of one or more proteins encoded by the target sequence. In another example, the cargo cleaves the target sequence and optionally inserts a further nucleic acid sequence into the genomic sequence of the subject. In yet another example, the cargo activates the target sequence. Any useful target sequence can be modulated.

Methods of treating patients or subjects in need for a particular disease state or infection can include administration an effective amount of a pharmaceutical composition having a plurality of constructs (e.g., any described herein). Additional methods include diagnostic methods, which can include administering an effective amount of a population of diagnostic particles to a subject in need thereof. In some embodiments, the population of particles, or a portion thereof, includes a ligand (e.g., to bind to target cells) and a reporter (e.g., to indicate binding to the target cell), whereupon the binding of one or more particles to cells as evidenced by the reporter component (moiety) will enable a diagnosis of the existence of a disease state in the subject.

In accordance with the present invention, there may be employed conventional molecular biology, microbiology, and recombinant DNA techniques within the skill of the art. Such techniques are explained fully in the literature. See, e.g., Sambrook et al, 2001, “Molecular Cloning: A Laboratory Manual”; Ausubel, ed., 1994, “Current Protocols in Molecular Biology” Volumes I-III; Celis, ed., 1994, “Cell Biology: A Laboratory Handbook” Volumes I-III; Coligan, ed., 1994, “Current Protocols in Immunology” Volumes I-III; Gait ed., 1984, “Oligonucleotide Synthesis”; Hames & Higgins eds., 1985, “Nucleic Acid Hybridization”; Hames & Higgins, eds., 1984, “Transcription And Translation”; Freshney, ed., 1986, “Animal Cell Culture”; IRL.

The present invention also relates to methods of fabricating a construct (e.g., or a population of particles). The method can include, e.g., providing a core (including a plurality of cores) having any useful characteristic (e.g., any described herein, such as having a dimension greater than about 50 nm, having a negative charge, having one or more pores, and/or including a silica); incubating the core with one or more cargo (e.g., any herein, including a plasmid, a CRISPR component, etc.), thereby providing a loaded core; and exposing the loaded core to a lipid formulation (e.g., any described herein).

In other embodiments, the method can include providing a core and then expanding the pores present on the core. In some instance, a method can include: providing a core including an external surface and a plurality of pores in fluidic communication with the external surface (e.g., where an average dimension of the plurality of pores is characterized by a first dimension); expanding the pores (e.g., thereby providing a core comprising a plurality of expanded pores, wherein an average dimension of the plurality of expanded pores is characterized by a second dimension that is greater than the first dimension); incubating the core with one or more cargo, thereby providing a loaded core; and exposing the loaded core to a polymer formulation or a lipid formulation to form an outer layer supported upon the external surface of the core (e.g., thereby providing the construct).

Examples Example 1: Preparation of Expanded Pore Mesoporous Silica Nanoparticles (EP-MSNPs)

MSNPs can be generated in any useful process, and then the pores for the MSNPs can be expanded by use of swelling agents. In particular, we pursued aerosol-generated MSNPs and solution-based synthesis of MSNPs.

Aerosol-based synthesis provided a high throughput process with controllable nanoparticle structure and features, but particles displayed polydispersity in size (FIG. 2A). Cetyl trimethylammonium bromide (CTAB) was employed as the template and removed by refluxing overnight. Employing a swelling agent provided particles having enlarged pores (FIG. 2B, BET surface area of 221.3 m²/g, BJH adsorption pore size of 13.2 nm, and BJH desorption pore size of 11.9 nm). Pore expansion was conducted with 1,3,5-trimethylbenzene (TMB) in a Parr bomb at 140° C. for 4 days.

Solution-based synthesis can also be used to produce CTAB-templated particles (FIG. 2C), in which CTAB was removed by refluxing. Pore expansion was conducted with TMB at 160° C. for 2 days. Employing a swelling agent provided particles having enlarged pores (FIG. 2D, BET surface area of 120 m²/g, BJH adsorption pore size of 12.4 nm, and BJH desorption pore size of 11.7 nm).

Example 2: Attachment of a Cleavable Spacer to Glass Beads

Expanded pore particles were further employed to install spacers, which in turn can be used to attach cargo to the core. In particular, we explored the use of a spacer configured to release the cargo upon a change of condition. For instance, in the presence of a reducing agent such as glutathione (GSH), a disulfide —SS— bond can be reduced to thiol groups —SH. If a spacer included such a disulfide bond, then the presence of GSH can result in cleaving of the spacer, thereby releasing the cargo from the core. Thus, we investigated the use of a spacer (FIG. 3A) having a disulfide bond that be reduced in intracellular environments that generally include GSH.

Release studies were conducted for GFP attached to 5 μm glass beads by way of a spacer (FIG. 3B). Upon exposure of 5 mM GSH, the observed relative fluorescence decreased, as compared to control lacking GSH. These data show release of the cargo (GFP) upon exposure to an agent typically present within mammalian cells (GSH), thereby allowing the possibility of triggerable release of a cargo upon internalization within a cell.

Example 3: Characterization of Cargo-Loaded EP-MSNPs

Further studies were conducted with EP-MSNPs and attachment of a cargo to EP-MSNPs. In particular, His-tagged GFP were attached to EP-MSNPs by way of a Ni-NTA-based spacer (FIG. 4A-4D). Without the lipid layer, GFP-loaded EP-MSNPs displayed aggregation characteristics (FIG. 4A,4C). Use of a lipid bilayer displayed reduced aggregation (FIG. 4B) and even recovered particle size (FIG. 4D).

We also characterized the effect of cargo and the composition of the outer layer on particle size (FIG. 5). Using His-tagged GFP as the cargo, a bilayer lipid coating improved colloidal structure and stability. When His-tagged Cas9 was loaded onto Ni-NTA-MSNPs using same procedure for GFP, the resultant particles did not aggregate strongly even without an outer lipid layer. RNP-loaded EP-MSNPs (by way of a Ni-NTA spacer) displayed some stability in buffer but exhibited signs of some aggregation, and one exemplary method to reduce aggregation can be to provide an outer layer (e.g., a lipid layer) for the RNP-loaded particle.

Any useful cargo can be employed. In particular, we characterized CRISPR reagents for nanoparticle delivery (FIG. 6A-6B). Cas9 release and activity from aerosol generated EP-MSNP were also determined (FIG. 7A-7B). A reducing environment with GSH did not release Cas9, as assay activity was observed with particles but not in the supernatant.

Example 4: Cellular Delivery of RNP Via EP-MSNPs

Cellular delivery of CRISPR ribonucleoprotein (RNP) was determined by use of a CRISPR cell reporter construct (see, e.g., Ramakrishna S et al., Nature Commun. 2014; 5:3378). In brief, effective RNP delivery to a target sequence of a surrogate reporter results in a frame-shift mutation, which in turn results in expression of GFP. The delivery system included providing a nanoparticle core (NP), attaching a spacer, and loading RNP, thereby providing a construct in which the RNP is attached to the NP by way of a spacer (FIG. 8A). The construct can then be delivered to a cell, and effective RNP delivery can be observed by the cell reporter construct (FIG. 8B), in which in vitro editing results in GFP expression.

FIG. 8C provides delivery of a construct that resulted in expression of GFP from an AAVS1 reporter target in 293T cells. The construct included RNP-loaded EP-MSNPs, which further included a Ni-NTA spacer between the cargo and the core. The RNP included a complex between His-tagged Cas9 bound with guide RNA (gRNA).

Example 5: Non-Limiting Method for RNP-Loaded EP-MSNPs

The functionalized EP-MSNP can be prepared through any useful process, first using an aerosol route to generate ˜200 nm diameter particles with 2-5 nm diameter pores. Through a pore swelling technique involving high temperature (160° C.) in an aromatic hydrocarbon solvent (mesitylene or 1,3,5-trimethylbenzene), the pore diameters were expanded to ˜12 nm. The particles were then functionalized using a slightly modified protocol described in Han D H et al., Nature Comm. 2014; 5:5633.

Briefly, the silica particles were treated with 3-aminopropyltriethoxysilane (APTES), followed by reaction with 3,3′-dithiodipropionic acid di(N-hydroxysuccinimide ester) (DTSP), then by N,N-bis(carboxymethyl)-L-lysine hydrate. The NTA-functionalized particles were then soaked in an aqueous solution of NiCl₂ to load the NTA groups with Ni(II). The disulfide of the DTSP group provides a route to detach the his-tagged bound RNPs from the nanoparticle through the reducing environment of the cell. That is, the disulfide bond is reduced by high concentration of glutathione in the cell (˜7 mM) resulting in cleavage of the tether with the formation of two thiols, one on the nanoparticle and the other on the now detached His-tagged RNP.

RNP preparation: Cas9 protein was produced and purified using a slightly modified protocol described in Zuris et al (Nature Biotechnol., 2015, 73-80). Single guide RNAs were designed following protocols and guidelines from the Corn lab (protocols.io/view/In-vitro-transcription-of-guide-RNAs-exabfie), using Thermo's T7 High Yield RNA synthesis kit and Ambien's MEGAclear transcription clean up kit, following the manufacturer's suggested protocols. Cas9 and sgRNA were allowed to complex at a 1:1 molarity ratio at 25° C. for 15 minutes, prior to RNP loading.

RNP loading into the delivery vehicle: The RNPs were exposed to the Ni-NTA functionalized EP-MSNP for short time (˜1 hour), and the excess RNPs removed via washing using cycles of centrifugation, removal of supernatant, and resuspension of the particles in fresh solution to finally yield the NanoCRISPR delivery vehicle.

Cell uptake and gene editing: RNP-loaded particles were resuspended into OptiMEM™ cell media, and then directly added to a confluent monolayer of cells stably expressing the fluorescent-reporter gene. After five hours, cells were washed with PBS to remove unabsorbed particles and given fresh media. Effective gene editing is assessed in two ways. First, by the induction of GFP. Cell cultures are examined by fluorescence microscopy, and after 72 hours, analyzed via quantitative flow cytometry. The second method looks directly at DNA editing, by extracting genomic DNA at the 72 hour time point, and doing T7E1 assay to assess effective gene editing levels (see, e.g., Vouillot L et al., G3 (Bethesda) 2015; 5:407-15).

Example 6: Delivery of Cas9 to Mammalian Cells

Lipid-coated mesoporous silica nanoparticles were employed to deliver Cas9 into mammalian cells via a controllable spacer. In this non-limiting instance, the spacer includes a reducible di-sulfide linking group, in which incubation with a cleaving agent (e.g., a reducing agent) resulted in controllable cleavage of the linking group and, thus, controllable release of cargo.

The tested spacer included a first linking group attached to the nanoparticle (e.g., a poly(ethylene glycol) group, such as —(OCH₂CH₂)₇— or PEG7), a second linker group for attachment to the cargo (e.g., a poly(ethylene glycol) group with a reactive group (NTA) and a nickel cation, such as —(OCH₂CH₂)₇—NTA-Ni—), and a cleavable moiety disposed between the first and second linking groups (e.g., a —S—S— group). The tested cargo included an RNP (e.g., a 6XHis-tagged Cas9 protein complexed with guide RNA).

As seen in FIG. 9A, MSNP cores were functionalized with a spacer (PEG-Ni-NTA disulfide linker) in order to attach a cargo (e.g., an RNP). The spacer included a reactive NTA group to bind to a nickel cation, which in turn couples to one or more polyhistidine tags (e.g., a polyhistidine tag having at least six histidine residues (6XHis) at the N- or C-terminus of a protein). The spacer also included a cleavable moiety, which is capable of being cleaved in the presence of a cleaving agent to separate the particle from the cargo.

Table 1 provides characteristics of various reducible particles, including MSNPs having a linker (MSNP-PEG7-SS-PEG7-NTA), MSNPs having a linker that further includes a nickel cation (MSNP-PEG7-SS-PEG7-Ni-NTA), MSNPs having a linker coupled to an RNP (MSNP-PEG7-SS-PEG7-Ni-NTA-Cas9-6XHIS), and lipid-coated (LC) MSNPs having a linker coupled to an RNP (LC-MSNP-PEG7-SS-PEG7-Ni-NTA-Cas9-6XHIS). As can be seen, particles were stabilized by cationic-based lipid coatings (LC), as indicated by a smaller polydispersity index (PDI) compared to particles without LCs.

TABLE 1 Characteristics of particles Z-average Zeta diameter potential Particle type [nm] PDI [mV] MSNP-PEG7-SS-PEG7-NTA 174.6 0.112 −38.9 MSNP-PEG7-SS-PEG7-Ni- 968.70 0.53 +5.23 NTA MSNP-PEG7-SS-PEG7-Ni- 332.80 0.45 NA NTA-Cas9-6XHIS LC-MSNP-PEG7-SS-PEG7- 302.00 0.22 NA Ni-NTA-Cas9-6XHIS

As seen in FIG. 9B, LC-MSN-PEG7-SS-PEG7-Ni-NTA-RNP were incubated with (+) and without (−) a reducing agent (e.g., dithiothreitol, DTT), and then NPs were pelleted via centrifugation. The supernatants and pelleted MSNPs fractions were analyzed using gel electrophoresis and indicated Cas9/gRNA RNPs were released only under reducing conditions.

Delivery of lipid coated particles were tested. As seen in FIG. 9C, lipid-coated reducible RNP complexed NPs were incubated with mammalian cell cultures (A549 cells) for 24 hours, and labeled Cas9 was internalized but not co-localized with endosomes.

Other Embodiments

All publications, patents, and patent applications mentioned in this specification are incorporated herein by reference to the same extent as if each independent publication or patent application was specifically and individually indicated to be incorporated by reference.

While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure that come within known or customary practice within the art to which the invention pertains and may be applied to the essential features hereinbefore set forth, and follows in the scope of the claims.

Other embodiments are within the claims. 

The invention claimed is:
 1. A construct comprising: a core comprising an external surface and a plurality of pores in fluidic communication with the external surface, wherein an average dimension of the plurality of pores is greater than about 5 nm, and wherein the core is a mesoporous nanoparticle; a spacer disposed within at least one of the plurality of pores of the mesoporous nanoparticle and/or disposed upon the external surface of the mesoporous nanoparticle; a cargo attached to the spacer; and an outer layer disposed upon the external surface of the core, wherein the outer layer is cationic and comprises one or more of a lipid, a polymer, or a combination thereof; wherein the spacer comprises: a first linking group attached to the core, a second linking group attached to the cargo that includes a reactive group and a metal cation, and a cleavable moiety between the first and second linking groups; wherein the cargo comprises a Cas9 protein complexed with guide RNA; wherein the first linking group includes a poly(ethylene glycol) group and the second linking group includes a poly(ethylene glycol) group with the reactive group and the metal cation.
 2. The construct of claim 1, wherein the core comprises a mesoporous silica nanoparticle.
 3. The construct of claim 1, wherein the average dimension of the plurality of pores is of from about 5 nm to about 30 nm.
 4. The construct of claim 1, wherein the spacer comprises a covalent bond to a functional group present on the cargo.
 5. The construct of claim 4, wherein the functional group comprises heteroaryl, imidazolyl, amino, amido, carboxyl, thiol, histidine, lysine, or cysteine.
 6. The construct of claim 1, wherein the lipid layer comprises a cationic lipid, a pegylated lipid, a zwitterionic lipid, and/or a cholesterol.
 7. The construct of claim 6, further comprising one or more moieties provided on an external surface of the outer layer.
 8. The construct of claim 7, wherein the one or more moieties is selected from the group of a targeting ligand.
 9. The construct of claim 1, wherein the spacer is disposed within the at least one of the plurality of pores.
 10. The construct of claim 1, wherein the reactive group and nickel cation is the divalent group: —(OCH₂CH₂)₇—NTA-Ni—, and the cleavable moiety is a disulfide group.
 11. The construct of claim 1, wherein the spacer comprises a coordination bond to a functional group present on the cargo.
 12. The construct of claim 1, wherein the construct has a polydispersity index of about 0.05 to 0.22 measured by dynamic light scattering.
 13. A construct comprising: a core comprising an external surface and a plurality of pores in fluidic communication with the external surface, wherein an average dimension of the plurality of pores is greater than about 5 nm, and wherein the core is a mesoporous silica nanoparticle; a spacer disposed within at least one of the plurality of pores of the mesoporous nanoparticle; a cargo attached to the spacer, wherein the cargo comprises a CRISPR component or a nucleic acid sequence encoding a CRISPR component; and an outer layer disposed upon the external surface of the core, wherein the outer layer is cationic and comprises a lipid, a polymer, or a combination thereof; wherein the spacer comprises: a first linking group attached to the core, a second linking group attached to the cargo that includes a reactive group and a metal cation, and a cleavable moiety between the first and second linking groups; wherein the first linking group includes a poly(ethylene glycol) group and the second linking group includes a poly(ethylene glycol) group with the reactive group and the metal cation; wherein the reactive group and metal cation is the divalent group: —(OCH₂CH₂)₇—NTA-Ni—, and the cleavable moiety is a disulfide group.
 14. The construct of claim 13, wherein the spacer comprises a covalent bond or a coordination bond to a functional group present on the cargo.
 15. The construct of claim 14, wherein the functional group comprises heteroaryl, imidazolyl, amino, amido, carboxyl, thiol, histidine, lysine, or cysteine.
 16. A construct comprising: a core comprising an external surface and a plurality of pores in fluidic communication with the external surface, wherein an average dimension of the plurality of pores is greater than about 5 nm, and wherein the core is a mesoporous nanoparticle; a spacer disposed within at least one of the plurality of pores of the mesoporous nanoparticle and/or disposed upon the external surface of the mesoporous nanoparticle; a cargo attached to the spacer; and an outer layer disposed upon the external surface of the core, wherein the outer layer comprises one or more of a lipid, a polymer, or a combination thereof; wherein the spacer comprises a covalent bond to a functional group present on the cargo, and the spacer is selected from the group consisting of formulas (ii), (iii), and (iv):

wherein Lk is a linking group, the circle arc is the core, and the wavy line indicates the cargo.
 17. The construct of claim 16, wherein the spacer is formula (ii):


18. The construct of claim 16, wherein the spacer is formula (iii):


19. The construct of claim 16, wherein the spacer is formula (iv):


20. The construct of claim 16, wherein the construct has a polydispersity index of about 0.05 to 0.22 measured by dynamic light scattering. 